Hi,
Assuming you are running your betson from the VGA port on your PC, then the PAL/NTSC is irrelevant.
Graphics cards are not physically capable of outputting PAL or NTSC TV signals via the VGA connector - only via the composite TV-out connector (if they have one).
Running Zsnes fullscreen (as I assume you are) - Zsnes simply uses/chooses a display mode that you set (probably in its menus) or autochooses one available in windows. (ie one compatible with your monitor).
So basically, you are safe - Zsnes is just an app and you can run PAL/NTSC games no problem - it does not generate PAL/NTSC output.