I can understand maybe registering a Marlin as there are quite a few of those out there, but in general the hovercraft community is small and the craft are too well known, so if a hover was stolen it would be too hot to handle. For instance there are 4 Otters, probably only about half a dozen surveyors, a couple of vanguards, a couple of explorers, I know of 3 prospectors, less than a dozen TS3's ect. You get the point
With boats, there are thousands of them, so easier to steal and sell on.
If you were using your hovercraft abroad, then that would be another good reason to register it,