Recently playing an assassin I was ranking for a while using my hands only in an attempt to better unarmed. What struck me as odd is the fact that I was able to get better at parry and it not affect my unarmed skill level, I was thinking that if I can get better at parrying with my hands shouldn't this also affect unarmed as that is what i would be using to parry with? I would thinking the same with ironhands aswell.

Nope. When you're using a skill that helps you parry with your bare hands, you may improve either at Parry or the unarmed skill in question, or both.

valguarnera@carrionfields.com