Also safety reasons. It is most people's metabolic low point, where mental functioning is quantifiably impaired. So, good idea not to be doing landings and takeoffs during that time.

But a pilot working at 3am is not "most people", and, presumably, would be on a very different metabolic schedule, no?

combination of low demand and the fact that for an airlines to have only a single flight at this time it means keeping desk and gate staff for only 1 or 2 flights that probably wont ever be full except peak travel season