Somehow you've managed to lose the exported face data, which either means you've installed a number of mods that didn't include that data, or your Textures.bsa is corrupted.
Are you certain it's all NPCs?
Yes, and it's not mods. I play on PS3. They arent grey as in no textures. It's more like.....their skin is paled or greyed. It's really annoying. I'd take a pic, but imagine them to have a normal skin texture, but instead of that healthy imperial skin tone, it's a sort of bleak grey skin tone.
Edit: It may not be ALL NPCs. I've noticed some females still have their healthy default skin tone. It's mostly males and some females.