Well, we do have proof of them eating/drinking because in Bionicle Adventures #5 Nokama drank from the water around Mata Nui, after the Toa Metru discovered it. What we don't know is how. It doesn't seem like they take off their masks before, but does the food/drink pass through their masks, or what?
Most masks seem to have mouth holes.
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For the brains, I lean toward a hard drive type system for memory storage at least, considering how easily MUians can be wiped of their memories. It's possible that they have organic components that interface with that, or maybe a combination of organic and mechanical. If the latter, that might explain the GB's confusion - they might have underestimated the amount of organic components needed for full sapience. 
Given that this is a world with protodermic powers, that doesn't necessarily imply any particular design for how the wiped memories were stored. For any method of storage there could be a protodermic power designed to erase that type of storage. Our organic brains could theoretically have memories wiped as well, it's just that there's no mechanism to do it so efficiently in our world (as far as I recall, lol irony!).
In fact I'd prefer the organic theory there too because some things that are their strongest memories in terms of neurology, especially language, are usually not wiped. Amnesia is often like that (although that's not a wipe but a block, as far as I know). That's because the neuron connections we use the most grow the strongest, just like muscular exercise and the like, and language is used more than virtually anything else, so even a strong emotional memory can be lost while language connections are retained. If it was a single hard drive type memory storage that would be rather odd (though possible by partitioning or even multiple drives).
I'm still a little unclear as to how our brains store information, been trying to find answers to that recently by coincidence, but it seems it's literally the physical arrangements of the connections between neurons that equals the storage.
So amnesia is just (as far as I know, again) the breaking of looser connections between a region of stronger connections, which in turn store memories. The basic reason getting hit on your head can't wipe your memories is because the connections inside that region are too strong; if you were hit hard enough to break those, you'd be dead just from the impact itself. But if something, such as a genetically engineered virus, were to destroy all those connections without killing you, you could apparently be mindwiped (maybe that's what some memory diseases do, I don't know, haven't been curious enough to read that deeply about it yet lol).
Also, hard drive storage is famous for not really being permanent, as seen on TV shows like NCIS and the like.
Re: mouth holes -- Noble Huna is one that doesn't seem to be good for drinking (movie form), but other movie form masks are clearly given a mouth that would work just like ours even when in set form it's not that obvious, yeah. Not really sure how the Huna type masks are explained. I doubt they take their masks off to drink; that's dangerous. Perhaps they simply use a straw. 
Edited by bonesiii, Mar 04 2013 - 07:43 PM.