I'm convinced that this doesn't happen on residences. At least not commonly. I have a friend who's really mad about boats, he even has a boat floor on his residence so if boats would de-spawn then he'd know about it for sure. So far I haven't seen this happening (note: we're talking about boats which merely float in the water somewhere on his residence).
This is in wilderness. town is a strange place i only visit sometimes. But io get the idea boat's disappeared. the already looked to fill up with wtare before.