Hi Alex -
The power cables for the GPS going to the battery have a small 2A fuse inline, so if there were such a surge that would be enough to damage the GPS, the fuse would go before the GPS did. I've never blown that fuse on any of my bikes, though.
Here's a link to the cable that I have installed on the ninjette:
http://www.cycoactive.com/gps/powint.htm