Oh....um....how are you supposed to keep mood up in late game then? I'm doing everything I can think of to improve mood.
You have to build more Cells for Pleasure and/or Breeding. The higher the number of Troops you have the more entertainment they need.
Reducing the number of Troops you have by doing Raids can help short term.
you can also trade troops for ration to reduce their number, if you run out of food, your troops die, and mood tanks a lot from that. so trading troops for ration fixes those issue by alot.