My two handed nord favors war-hammers but my question is about the skull-crusher perk, if it ignored 25% of armor, does this apply to creatures that don't look like they are wearing armor like dragons and trolls?, or it only applies to armor-wearing enemies?

Well, it would technically apply to any enemy that has an armor rating. That being said, very few bad guys have any real armor, and even fewer (if any) have any armor related perks. Therefor, the Skull Crusher/Limb Splitter perks are of limited use. However, I have taken them with my current character that does not use any smithing and it does help, especially with boss level enemies, which at least usually are wearing some armor.