Our club has been looking at using this system for a couple of years now. The pick-up loop is the major problem with using the transponders. It has been used underwater for jet ski racing, but their's is in a pvc tube floating on the surface. Because the jet ski's use a pump, there is no rudder, prop, turn fin to deal with. You could string it over the startline, but then you have to deal with possible boats hitting it. The personal transponders will pick up at quite a distance. I race 1/12 scale over the winter, and I heald my car over my head and it still picked it up. We have also purchased RC Scoring Pro software which can be adapted to boat racing format.
The next possible solution is RFID tags. They are cheap, but the downfall is the speed of the boats. I don't think they would pick up a boat going over 70 mph.
Yes....it is 2012. And we need to step forward. It would take a large investment to even try this system. I hope someone does.