MAME would probably be ok, as long as you don't need both screens going at once (MAME can't even clone displays properly, let alone running two things at once). But other emulators might have problems targeting a particular display, and other issues as well. Making sure all the controls and joysticks stay in order can be tricky.
I have a cab that has a vertical CRT in it, but the video output can be physically switched over to a horizontal driving cab. Other than using a physical switch, i wouldn't do it. I tried, and there were all sorts of issues.