I've done top-of-dash mounts before, including on my current car. I like that it places the radio where I don't have to look away from the road to see it, and where it won't break my (or my passenger's) knees in an accident. Cons are that it does visible damage to the dash (if you remove the radio later to sell the car, say) and running the wiring can be a little more challenging. It's certainly much better than having the radio loose on the seat, as far as crash safety goes.
I haven't had any issue with overheating with my radios, but I agree the possibility is there.
I no longer see theft as a big issue. Thieves generally aren't going to know what an amateur radio transceiver is; they'll be looking for expensive stereos, smart phones, or GPS units that can be easily grabbed.
The important thing is to make sure you've anchored the radio to a solid, metal part of the dash. This isn't *usually* too big a problem because most dashes are largely metal under the padding, for crash safety reasons. I prefer to use through-bolts and lock washers, the biggest size that will fit through the radio's mounting bracket. If access is restricted large self-tapping screws will work, but make sure they get a good 'bite' into the metal. If it starts to loosen, not only is it a crash hazard, but the rattling will drive you insane. (Stage roads can loosen up almost anything. Blue Loctite is not overkill.)
Investigate what's under the spot you're drilling into before you start drilling...hitting a dash wiring harness with the drill really sucks.

On cars with passenger side airbags you have to be careful the radio doesn't end up in the deployment area. On cars without airbags, try to put the radio where the passenger won't hit their head on it in an accident. My Mercedes had a great spot on the dash tray right next to the instrument binnacle.
For wiring, I ran the coax along the windshield seal up into the headliner; the power wiring runs through the trough between the dash and the windshield over to the side of the dash, where there was an existing hole next to the A pillar. Another simple and inconspicuous method on some cars is to drill a small hole through the defroster duct, under the dash, and run the wires up through it.