OK according to the wiki:

http://geck.gamesas.com/index.php/AddPerk

You can give perks to NPCs. However I currently have a script to walk through the actors in a cell and give them a perk. I am checking to see if they already have it by using the "tempRef.HasPerk xxxx" but it always comes back as false. I even added a damage health over time which does massive damage and kills me if I add it to myself but does nothing for NPCs.

Can you add perks to NPCs?

I don't know for certain whether or not NPCs can have perks, but they definitely don't work for NPCs. If you want to store some data on an actor, just use a token. If you want the functionality of a perk, you'll need to find another way to implement it.

Cipscis

There was a mod that added perks to creatures. Although I'm not sure if the effects were faked and made through a script.

Hmm. I added the toughness perk to some NPCs and I swear they took less damage/required more hits to kill than equivalent ones without the perk. But I didn't do an indepth study.

You can add, remove, and test for the presence of a perk on NPCs. The entry points have no effect, though.