Is NPC death permanent?
From one playthrough, I can have seen that it is always or almost always the case that NPC death is permanent. I haven't seen evidence to the contrary yet.
I've completed multiple (10+) play-thrus and every NPC stays dead or gone, the bodies of your PC's that die will stay until looted as well.
So you after clearing you can safely send unarmed people in to pick the goodies.
I've not played enough to know if any locations have additional mini-story-arcs that may bring more NPC's to the location at a later time but I've not seen one yet.