I drilled ventilation holes in my trapdoor cover right where the processor chip is. But it's a Cobra 030 and it fits. Dunno if you have the option of doing the same for an Apollo 040 for the bits that stick out. I guess it's not worth the effort.
The lower the mhz the lower the heat, generally.
Dunno if decent(cheap) and Apollo 040 can be said in the same sentence though. Unless it's a damaged one.