Is it ok to place an AirPort Extreme base station on top of a Mac mini, or could this cause problems (like overheating or interference) with either device?
As depicted, they do fit together pretty well...
I advise you to avoid to put your Extreme AirPort Base station on top of the MacMini, because the top of the Mac mini is a wireless reflector (cases of hard disk and optical drive are flat metal surfaces).
In the field of wireless network you should imagine each wireless card as a bulb light. To have a smoothly working wireless network, all these bulb lights should be placed apart from each others. You should avoid to place them against a reflecting surface (flat piece of metal, a window, a concrete wall, on a glass table…) or behind an opaque object (metal, glass, concrete, us i.e. humans…) who will create shadows.
When you place a wireless antenna directly against a reflecting surface it will suffer of interferences reflected by this surface (the direct field and the reflected one are using the same carrier wave and they fully interfere with each other).
If you would like to learn more about this interference problem, I advise you to install iStumbler on a portable Mac and to compare the signal & noise columns (on iStumbler) when:
Stacking is not recommended. According to the Mac Mini user guide it is not recommended to place anything on a top of a Mac Mini, since its can interfere with the Mac Mini's Antennas for Wifi, Bluetooth and optical drive operation. Additionally, since that area kind of gets hot on my Mac Mini Late 2009, its probably not a good idea to cover it, since the Mini would be adding heat directly to the bottom of the Airport Base Station as well, and it does not have fans to keep it cool.
As noted in Mac Mini Late 2009 User Guide
In your case a stacking solution (pictured below) might be the safest way to save space and keep your hardware on the safe side to the written letter in the book. But if your careful and things are not interfering and things are not getting too hot, stacking might be OK, contact Apple to be certain.
Also consider moving your Airport Extreme to another location, it might help avoid sources of wireless interference at your desk, eg monitor, computer, speakers, cell phones, etc. You might be able to mount the Airport Extreme behind your desk or to a nearby wall behind your desk to get it out of the way and reduce the need to stack things.
If I had to do it, I'd stack them with some kind of spacers to allow some air circulation between them.