Darknuts are called Tart Knuckles in Japan which makes me think they are just another variant of the same thing. Could just be that Tart Knuckles use swords and Iron Knuckles use axes. I think brainwashing is present with all knuckles. In WW their eyes are a single colour as though possessed...
The character models do show Gerudo forms inside though these were removed in the 3DS versions of the game.
Due to the Gerudo pattern on their cloth I am still inclined to think they are Gerudo in origin and possibly those that have been brainwashed by Twinrova just as Nabooru was. I would...