So my wisdom teeth extraction holes are finally closing what happens if there's still food in it when it fully heals, is that okay?

Okay: The healing process will expel any food or other material that may be in the hole. Do not worry about food getting trapped in the holes.

See your surgeon: If food debris is left in the socket, over time it will become infected and an abscess or swelling will develope. It usually occurs on younger patients due to faster healing process. Usually food debris cause irritation prompting you to clean the socket. It is rare for food debis to remain trapped in the healing process. If that hapens, it can be treated by your surgeon.