I have this same issue but can confirm that, whatever the problem is, it has nothing to do with Hookers Of The Commonwealth. I know this because I don't use that mod and yet Arturo, Trudy and a few other unnamed NPCs (so far in my playthrough) have this issue. It can't be anything to do with CBBE because it affects both male and female NPCs. Hmmm, most perplexing. I don't see how Eli's Armour Compendium can affect NPCs cus as far as I know, it doesn't force any outfits onto them. Am I mistaken about that?