Well, the Water Beetle is an old trawler, surrounded by water (partially submerged), so it does make a degree of sense that it wouldn't be affected the same way. Those types of engines are significantly more durable than most land vehicle engines (for example, boat engines are typically used way less often than a car's is, and I'm sure we've all seen what happens when you don't drive an old car for a month or two in the winter, and that's without talking about the battery). They have to resist salt water corrosion, etc. But the main thing is that the seacock on the Water Beetle was probably open (I really doubt Thomas closed it), and there was almost certainly a lot of water in the engine's cooling systems that helped keep it operational.
Also boat diesel is expensive, and boats are money pits. I got rid of my sailboat many years ago and haven't looked back. It was not nearly the chick magnet I was hoping it would be.