'If yes' doesn't sound natural. We would understand it, obviously, but a native speaker would be unlikely to say 'If yes' or 'If no'. We would either say 'If so' or 'If not', or echo the subject and auxiliary verb. For example: Do you have a European Community passport? If you do, you can go straight through customs. If you don't, you'll need to wait here to have your passport stamped.

Not always. It depends on the context. "If yes" would sound awkward in many cases.