I had an Apollo 040/40MHz in my desktop A1200 for quite some time. It does get hot, but I never experienced any overheating symptoms.
Then again, I always had the top cover off because the 1240 with it's big fan and heatsink and my 3.5" hard drive took up too much space. I also used some extra rubber feet underneath the computer, about five or seven millimeters thick, to keep the air flowing.
edit:
Oh yeah, I also had the trapdoor lid open at all times.
