The question is simple. Do you think enemy NPC′s (And maybe enemy creatures could have special perks) will use perks? That would add lots of variety to combat gameplay.
Also think about how attributes(Yes, the removed attributes) could play a role in resisting enemy perks, for example, if an enemy attacks you with the perk to make you bleed, you can resist it thanks to your resistance, which gives you a bonus against it.
Yes, I think enemies will have perks.
Because it will make combat more interesting, and also if they did not you would never meet a challenge again after a certain level.
Maybe it will be level and class based. For instance, a random enemy rogue of level seven would have seven rogue class perks.
For dagger efficiency maybe, or sneaking up on you.
But a hedgewizard will have perks boosting his destruction or to make his summons more powerful.