I'm going to reply a little out of order to start at the root of your reasoning. And sorry that some of this repeats what the other posts say, just wanna be crystal clear what I mean in-context.
If they were making Matoran masks, why would they bother using the proper disks?
Because you know some of your customers might be destined to be Toa, and upon finding out they're stuck with the wrong shape, trade it in for one made by a maskmaker who isn't lazy, and probably use their prestige as a Toa to warn people not to buy from you. And because being an honorable Matoran you value doing things right even if it means you can't cut certain corners.
Note: I'm here making an assumption that we can't be certain of. Read on.
Seems like a waste of material if you ask me. Juts carve it in the correct shape and call it a day.
This line seems to contradict the above. If you're carving it in a shape that doesn't go with the power of the disk you used, it's not the correct shape, right?
You are right to wonder as many have before whether it's a waste of material to mix powers, since half the mask of each disk disappears when two are mixed into one. But don't forget that often mixed powers are considered more useful for Toa to wear (and by mixing the right shape for Matoran, you're doing so for "potential future Toa"). So the benefit outweighs the loss. And presumably Mata Nui somehow makes new mass somewhere in the universe to counteract the loss.
The power leaks out of the mask after it is made, making it powerless, so it really isn't a Huna anymore is it, even if it does have the shape.
This line requires us to make an assumption with no evidence for it, that the function of a power's programming in a disk is deleted just because the energy-fuel for it is drained. But there is no evidence for that assumption. If I make a car, then drain its fuel tank, it is still a car. Just not one that will run in that state. Later when I refill the tank, it won't magically change into an airplane.
Of course, transformations of power are certainly possible in Bionicle. But there's no evidence it happens in this situation.
Surely Toa Power can't sense the shape of the mask
Why not? Protodermis is a super-advanced molecule that can run incredible powers without glitching, and with mental control! Being Toa-ized even gives you the body shape that you "think of as a Toa". Surely adding the right power to a mask that had (hypothetically) no power identity at all, based on the shape, would be very possible. Note that for reasons explained above, adding the power's function programming is not needed at this point. However, the protodermis apparently does have to know the shapes -- not even just the Matoran, but the molecules themselves.
I say this because the Toa Metru did not know the powers that went with their shapes, yet the Matoran versions of their shapes (or in Vakama's case, a Matoran version of the Noble shape) were transformed into the proper Great Shapes. Also, when they became Turaga the masks changed into the proper Noble shapes.
Therefore, yes, "Toa Power" (or protodermis's programming that runs during the transformation) surely can sense the shape of the mask (that would be easy) and even change the shape to the proper level-shape.
However, we don't know what the rules are for this, beyond what we've seen actually happen in-story. For example, in my response to the first quote above, what if protodermis would correct a bad maskmaker's mistake, changing the shape to match the power it already had? We can't rule this out per se. But it's also possible it is just automatically changing to the power-level version of whatever shape it detects with no check for power at all (due to reasons explained below).
Krakua's Hau-shaped Suletu would disprove that theory.
Not sure if it was ever given a reason in that specific case, but for Norik we were told that there was a tradition of having masks in the "wrong" shapes to honor elite Toa (who would know the powers well enough to not need to worry about the right shapes), by associating them with the masks of past heroes. So what is normally considered dangerously confusing for novice Toa is a high honor for them. (This is why I lean against protodermis automatically "fixing" shapes that are "wrong.")
Whether this is the case for Krakua I don't know. Three main possibilities come to mind:
1) The Order wanted him to have the honor that elite Toa do, intended to train him very well, sense great potential, etc.
2) If he got his mask from a corner-cutting maskmaker who did assume it didn't matter, and if protodermis would not correct the shape in that instance, he might be someone suffering from that as in the beginning of my reply.
3) The answer I suspect is for psychological and safety reasons -- if enemies see that he's wearing a Suletu, they'll likely consciously brace themselves for a mental invasion, possibly preventing him from learning what he needs to know (such as by concentrating on one thought to the exclusion of all else), and they might realize it means he's open to attack. But since they see a Hau, they might decide it's not worth shooting at him while he's watching them, and also fail to prevent mind-reading.
I would imagine that even though the power leaks out from a Kanohi made of level 6 or less Kanoka, some traces of the Kanohi's power still remains (If something conflicts this, please let me know).
Technically that answer could work, but it is also assuming that "the power" is just like a single substance. Every single molecule in the mask, whether it's charged up with "fuel" to Great or totally drained, has the programming to run the power. So I wouldn't use "trace" to describe that, really.
Note also that due to Vakama being a very good maskmaker and yet not knowing which powers went with the six Toa Metru shapes, it appears that maskmakers themselves might not always be the ones who actually mix the disks that are used in all cases. A Diskmaker could handle that, and (for example, as I have theorized before) stamp on a relief-carving of the basic shape-label (similar to the image of the Vahi on the Disk of Time), and maskmakers like Vakama would just go off of that, possibly putting their own signature twist on the shape (this latter bit is at least confirmed in Nuhrii's case). But somewhere along the line, the right mixture would have to be made.
Also note that prior to the invention of Kanoka disks they would likely have still mixed the right power, they just wouldn't be able to use disks to test that they got it right (but maybe they did let it solidify into some "pre-mask" solid shape first and test it then in the same way; unknown).