I haven't had the hovering bug (yet), but I've lost a couple boats to being docked too shallow... one, it can hit the bottom in a storm (or probably even just the regular waves), and two, it lets mobs pretty much walk right up to it and start hammering away easily.

Building a dock out can be a frustrating task given the limitations of the building system in the water, but it's worth it if you don't want to destroy/rebuild the ship every time. Plus there's something to be said for the aesthetics of a docked longboat in your base.