Im doing some experiments with Pocketlab and Arduino, Vacuum will get to around -30inHg. I tried with my raspberry pi and it just kept dying everytime a vacuum was pulled. The only problem I can image is the arduino heating up.
Interesting question. You're right- heat is your enemy. Given the power dissipated by a Pi even when idle I'm not surprised it died. Most chips depend on convection to get rid of heat. A loaded Pi might require a (convective) heat sink and/or fan to keep it's core temperature down to an acceptable level, and that's at normal pressure and temperature. An Arduino -might- be able to work in a vacuum- it can lose some of it's heat through lead conduction- it'll only draw ~.25 watts normally vs 2.5 watts plus for a loaded Pi.
Ultimately it will depend on your application. If you have idle time when you can put the Arduino to sleep that will help keep it cool. If you have a conductive heat sink you can use then that would certainly help.