Like Mike and KJ said, sometimes the permit is worth more than the boat. The only way to get a houseboat on lake Shasta is to buy one with a permit that will transfer. In this case, you will be paying $100,000 for a $50,000 boat and a permit that is worth the rest. As long as the boat continues to float it will still be worth the permit in five years.
On the delta there aren't any permits, so it is just the value of the boat. How much the boat depreciates is going to be a function of how well you maintain it. If you bought a boat that was at least a few years old and kept it in as good of shape as when you bought it then it would still be worth approximately the same after 5 years. Of course, you will have spent a fair amount on it over the five years to keep it that way.
On the other hand, if you ignore it and let small problems turn into big problems then the boat can lose a lot value. If you never haul the boat and paint the hull then you can end up with some major hull repairs. Leaks in the roof can rot the topsides and create major repairs. Carpets wear out, upholstery gets ripped, etc. etc.
If you want to keep a boat in reasonable condition then I would plan on spending about 10% of the boats value a year on upgrades and repair.