I still see the goo pile, but it says [EMPTY] when I try to search it. Sometimes, there's goo piles there when I didn't even shoot anyone in that area, so I wouldn't say they're necessarily enemies that will never respawn again, but maybe just decoration goo.
goo you didnt create yourself was created by some1 else with a power weapon never as far as i know is it window dressing.
I think you should be able to pick up goo/ ash piles what have you and drop them somewhere discreet so you dont have to see them, as I hated returning to mothership zeta and finding bodies and goo and ash all over the place on my fancy bridge of my ship, and they should have allowed more access to the ship after beating that alien invader stuff as far as that goes ...but I digress.