This is more speculation than theorizing, but feel free to move it to Theories if you see fit, mods.
Anywho, Iron Knuckles and Dark Nuts. What's under the armor? I always just thought they were hollow, with the exception of a brainwashed Nabooru posing as an Iron Knuckle. And as much as I hate to admit it, there is a face hiding behind the helms of The Wind Waker Dark Nuts, and that would suggest that there is a complete body in the armor.
I still like the idea of suits of armor enchanted to come to life, but I'd like to see what you all think about it.
Movin', moovin', movin', rawhide!
But anyway, under the armor... Magic would certainly seem to be involved; you'd think a huge tomahawk/axe/whatever-the-heck-it-is would be hard for anyone to wield and deal about three hearts' worth of damage. There would seem to be a viable host, however.
Eh, maybe there are different forms of each, some of the types being enchanted armor and hosted armor.
I think there's nothing behind the armor (save for the Nabooru Knuckle which you mentioned earlier). The face could easily be a physical manifestation of the magic and could just be there to add an even more unnerving aspect to the armor, when in reality it isn't even fully corporeal or even a true head, just a face.
In the Wind Waker, you can knock their armor off. They look like some kind of dog. An Anubis type of individual.
So, I know I'm necro-posting, but I thought I'd throw in my two cents.
I believe that since Windwaker is years and years and years after at least OOT/MM, and Ganon's power was depleted (er, well, at least, I don't think he's as strong as piggy Ganon ever was, and most of his power in WW came from swordskill rather than magic) as well as there being an entirely new population of enemies (and some enemies that adapted (a la floormasters and wizzrobes)), that perhaps both theories are correct.
In Ocarina of Time/Majora's Mask/etc., the darknuts were just possessed suits of armour because Ganon was not as feared/revered (everyone in WW knew about Ganon, though they didn't know his name; not that far of a stretch to think that the enemies knew about him too) and he was far more magically powerful. In WW, he was feared due to the whole "destroyed Hyrule forevers" and essentially causing the apocalypse, and probably got a few dedicated followers (the dog-like beings being race of beings that are enemies themselves; Ganon just gave them knives and armour to help kill Link) and so that is why there are things under their armours.