Ive actually gotten decapitated by chief bandits, so some enemies do have perks for their main skills. Dremora summons also decapitate enemies.
So maybe a chief bandit using a warhammer spawns with ranks in the armor ignore perk.
I've also been decapitated, and I've seen companions use the sneak role and watched enemies charge dual-cast spells before throwing them at me. Without being able to look at the data files in the Creation Kit, I can't yet know how that's handled. What I can say is that in Fallout 3 and New Vegas, perks absolutely could not be assigned to anyone but the player. Using AddPerk as a console command or in scripts wouldn't fail, but it also wouldn't do anything (and HasPerk would always return 0). You could fake it for some things by assigning enchantments or huge duration spell effects (spell effects with durations that last multiple real years won't glitch or anything), but things that required entry points to function couldn't be done, because those only worked with perks. For example, the Psycho chem in both of those games has no effect on anyone but the player, because what it does is add a hidden perk with a Calculate Weapon Damage multiply value 1.25 entry point. Now in Skyrim, it's obvious the perk system is built off of the perk system in those games, and using the AddPerk console command on NPCs seems to have no effect.
By the way, hilariously, the Turbo effect in New Vegas is actually just an actor value, and actor values apply to all NPCs. If you use the console to set any NPC's Turbo actor value to a positive integer (true), that character will zip around at insane speeds.