I haven't had my bags searched either time I've refused the Nude-o-Scope. I have refused to remove my shoes as well both times, and had my shoes swabbed..
My new strategy is to make sure I eat some stuff that will make me really gassy, and when the screener is running his hands over my butt, I'll let go with a hell of a fart. This is going to take a lot of timing and discipline of course, but it will be great once I get it all right.