I've only seen the Iron Knuckles in OOT+MM, so if they are different in any other games this idea may be wrong.

The differences between the IKs and Darknuts that I've seen are that the IKs use two handed weapons, axes specifically, while the DNs use single handed weapons, usually a sword, and a sheild.

But as to the idea of one becoming the other in a later age, they seem to be two different classes of knights. One could have replaced the other in use though.