well, they probably will
skyrim npcs had them kinda, but it ended up kinda redundant for the most part
like a bandit chief would have some perks that increased his light armor defense by a bit and his 1-hand damage, but since his high tier in the bandit ranking system already gave him beefy stats in health and light armor and damage, the perk was pretty much unnoticeable
the ebony warrior is the only one i can think of that had some scary perks in the vanilla game
i thought you meant you heard enemies would have 'tricks up their sleeves' as in active perks
it actually would be scary if, say, a raider bomber-freak had perks you could actually notice right away
(access to rare nuka grenades, a perk that doubled grenade throw distance, double explosion size, etc) you know things you could see and immediately think 'yep, that fracker has those scary explosives perks going on'
if enemies just have some passive buff perks that get lost in their existing abilities, meh, that's cool but not very exciting
fallout has some crazy abilities tied with perks, it'd be nice to see some enemies get the good/wacky ones like you, not just buffers