If a trailer is properly sealed off between animals, is it okay to have more than one type together for a long trip say if you are moving? I could see some being ok like a horse and dogs, but what about horses and donkeys?

If its completely sealed off I don't see what it should matter what is on the other side. So long as there is no worry about air circulation spreading diseases it should be ok.

I'd be worried that if you were moving animals of different sizes they might get trampled, or fall over or one might get startled. Animals have to fit their transports reasonably well because they don't have seatbelts.

If it were sealed off physically and the animals normally lived together, I wouldn't even worry about disease spread. Any of that would happen in their normal living together.