1) Not that I'm aware of.... at the very least, it works fine either way. I've never done any speed tests one way or the other, but my guess is they are nonexistant or minimal.
2) As long as your "JAMMA control panel" is in some way connected to a PC (more than likely through a JPAC), then yes, it is not a problem. Once you can get your computer to recognize the arcade controls as "keyboard presses" its just a matter of setting up your controls in your other emulators.
3) There are quite a few front ends that allow you to use multiple emulators and choose them at will. Do a quick search here. I use MameWah and like it very much. I'm almost positive that Dragon King does multiple emus, as well as Kymaera, Emulaxian, 3d Arcade, etc.
I've only personally used MameWah, but I'm pretty sure the others mentioned (as well as others I'm sure) have the multiple emu feature.