It was confirmed that the Turaga hid the masks, which they took from Metru Nui. As far as why Makuta/Teridax didn't destroy the masks, I think the explanation back then was overconfidence. Now, though, we can safely say it's part of his Plan - perhaps to make the Mata's defeat of him seem harder (as they might subconsciously think things like "I couldn't have done that without my Golden Kanohi")?
So I've been practicing my writing by rewriting the main Bionicle story with some differences, depending on what I feel works. Thinking about how I am going to handle some things, I've run into questions that some of you may or may not be able to help with. Rather than make a bunch of topics over time, I thought of as many as I could and compiled them all at once.
1. I'm assuming the Turaga hid the Great Kanohi on Mata Nui, so why didn't Makuta just destroy the masks? The masks were unnecessary to awaken Mata Nui, and there was no need to give the Toa more power. Maybe it amused him to let the Toa search for a tiny bit more power knowing it would not help them in the long run? Pretty minor question with no real effect, I'm just curious.
As far as that goes, I think that they were placed there by Teridax in order to aid the Mata (remember, the Brotherhood had a large supply of Exo-Toa, and they were invented in the MU, not by the Great Beings).
2. What was the purpose of the Exo-Toa in the Bahrag lair? My personal theory is that they were supposed to protect the Bahrag while they were asleep, but I have no evidence.
I don't believe any explanation has ever been given for this, though out-of-story it was obviously a way to get the Mata to realize "the power of TEAMWORK" again.
3. Why would Exo-Toa prevent the use of elemental powers?
That's actually the way I've theorized it, though Teridax could have ordered them to slow the Kal down in order to let the Nuva beat the Bohrok (after all, he was nearly or fully recovered by that point).
4. Why did the Exo-Toa in the Bahrag lair attack the Bohrok-Kal? Were they operating on the goals of the Toa Mata as the last people who used them?
Such as the Nuva Symbols and the random Kanohi Nuva everywhere?
A lot of the Bohrok Kal saga didn't make sense so I'll ignore it for now.
Possibly. However, BS01 states that his mask was lost. Not sure why some guard would grab the symbol but leave the masks... unless it was a split-second decision and the guard was all but walking on lava.
5. How did Tahu's Nuva symbol survive the destruction of the Suva? Did some quick-thinking guard grab it?
Although I don't think this was ever confirmed officially, there was a Toa Suva in Metru Nui. It's likely the Turaga based the Suvas off of that.
6. I assume the Suvas did not always exist on Mata Nui and the Turaga made them based on some prior knowledge?
I'm unsure as to how exactly they did this, but it's possible that they just moved the Nuva's masks (except for Tahu's, as they were... lightly toasted ) to the Metru Nui suva.
7. The Suvas on Mata Nui seemed to be attached to the ground, so I assume the Toa/Turaga simply carried the individual masks and Nuva symbols down to Metru Nui?
Yes. If I remember correctly, the Mata Nui Turaga used extra Noble Masks from their villages' Suva.
8. Could multiple Toa use the same Suva?
...I really have no idea. There's the possibility that he didn't want to claim any of the masks as his, though, and that he felt his Hau would be the most recognizable "face" for the Matoran.
9. Why didn't Lhikan use the Suva and abundance of masks in the Great Temple?
The Lhikan essentially sailed up a slowly-winding-upwards passage, which was actually just a tunnel network in Mata Nui's face. The Airships could probably just fly through one of the sunholes and come up in Po-Wahi somewhere.
10. How did travel between Mata Nui and Metru Nui work? I never understood this. The Toa Metru were able to get to Mata Nui by boat, yet Mata Nui is directly above Metru Nui. I assume the airships were able to fly through some cave systems in Mata Nui Robot's face to come out on the surface, but I never understood how they were able to sail upward.
There's the possibility that he just gambled on it, though I prefer the explanation that Teleportation discs get some general idea of their user's intent.
11. How did Vakama know the teleportation disk he launched at a fleeing Nuhrii would bring him closer and not send him further away?
You know Teridax... all those schemes within schemes...
12. What was the point of the Morbuzahk? I think I read on BSO1 it was supposed to drive all Matoran to the Coliseum where they would be encapsulated, but disguised as Dume, Teridax could just call an assembly to bring them all together, which is what he ended up doing, anyway.
In other words, nobody knows.
According to Time Trap, Teridax was distracted by having to deal with Nidhiki, Krekka, and Nivawk's minds at once after absorbing them, so he wasn't thinking straight.
13. Why didn't Makuta kill the Toa Metru? As far as I can tell, if all of the Matoran were encapsulated and the Metru dead, his plan would work just fine, and I don't think he should have had any trouble dispatching six inexperienced Toa. Instead he played a game of cross the street without getting hit by a car and got himself imprisoned.
I'm fairly sure that the prison prevented Kopaka from using his ice powers (though why he didn't just freeze Avak over without any kind of beam I have no idea).
14. When Avak trapped Kopaka in his mental prison, why didn't Kopaka attack Avak directly instead of focusing on the cage?
Axonn and Brutaka never really got fully defined abilities, though it can be assumed that Brutaka only has epic strength/Antidermis consumption naturally (though now he has a bunch of Makuta powers too...). It's also pretty safe to assume that Axonn can just turn his physical energy into any form of non-elemental energy, as he's only been shown to use various energy attacks (plus boomeranging axe, for some reason...).
15. Are the powers listed for Axonn and Brutaka the full extent of their abilities, or is it unknown exactly how much they can do? Again, just curiosity.
He sent them there as pawns, I believe, to try (and fail) to get the mask, but to give the Inika a hard time so they thought Teridax was actually trying to get the mask.
16. I may have overlooked this while reading the books, but why did Makuta send the Piraka to Voya Nui? Was it just to get himself into a position where he could directly affect event when things weren't going exactly how he wanted them to?
I'm fairly sure that there were some structures and such which were vital to Mata Nui's health (plus liquid protodermis purifaction and sollid proto reclamation, as you said), though the Metrutoran probably didn't know it.
Some Bigger questions:
16. How exactly did the Matoran's work in Metru Nui keep Mata Nui alive? They provided resources like tools, but they didn't seem to ever do anything that directly affected the Robot besides liquid protodermis purification and solid/molten protodermis reclamation. Because seriously, Po-Matoran carvers contributed absolutely nothing, as far as I can tell.
I'm not really sure if that was ever answered, though they may have been meant as part of the Great Beings' "Failsafes-R-Us." I think Nektann actually wondered about that at some point as well.
18. What was the purpose of any species other than Makuta, Matoran, and Rahi? Not including some one-offs like Karzahni, Artahka, Tren Krom, and some of the Hand of Artahka/OoMN members.
It was probably just maintenance, to be honest. Except for perhaps the Av-Matoran, who were apparently meant to become Toa (as stated by Antroz, who said something like "Av-Matoran have an unusually high potential to become Toa). (Ironically, there was only one Av-Toa who ever came into being )
19. What was the purpose of Matoran outside Metru Nui? I assume maintenance, but we never saw that happening and if they were maintenance crews, wouldn't it have been better if they knew why and what they were maintaining (Big Robot).
Since the GBs didn't plan on the Matoran becoming sentient, it was more likely a "they don't need to know" factor.
20. Why didn't anyone know they were in a big robot? Was it to prevent anyone from getting ideas like Makuta?
As far as I'm aware, yes. Of course, it's still massively overpowered, as almost every MU being both is made of and carries some form of metal.
21. Almost forgot. Does magnetism affect only magnetic substances (metals and magnetic rock)? So it would be mostly useless in a purely organic environment.
I've always thought that the Piraka's "extra powers" didn't get much thought. Reidak was totally invincible as long as he didn't die in one hit, Vezok could imitate as many powers as he liked, whenever he liked (and any powers, including elements), Avak could instantly and unbeatably imprison anyone as long as he knew their weaknesses and powers, Hakann could infinitely spam mental blasts and drive enemies insane at no cost to his own stamina, Thok could bring anything - even a mountain - to life, and Zaktan had no power but was made of a cloud of prodotites, which essentially made him immune to any attack he could anticipate and move enough of his body away from.
And while I'm making a long list of questions, I'm going to throw in some opinions as well:
Reidak's power is ridiculous and terribly defined.
Well, the Nuva eventually did win - in fact, Tahu overcame nearly all the Rahkshi in the MU in 2010's (confusing and rather dumb) story arc, and the Nuva's "interference" was instrumental in allowing Teridax to fufill his destiny.
Is anyone else frustrated by the fact that, in hindsight, the Toa Nuva never won? Every victory they had as a team was already predicted and expected/hoped for by Makuta. And they were the central characters of the story and were the most powerful Toa and everything. It's just kind of a downer whenever looking back at the story ever since Makuta took over the MU in 2008.