I only just started playing again recently but I remember losing boats no matter how hard I tried. There would always be a mob that somehow worked its way through walls, defences, etc., and smashed the boat. I used to disassemble them too for the sake of not losing materials.

To try and prevent that I am using Cheb's Necromancy mod (there's a Mercenary mod by the same author, where you can hire people for gold) and when I get around to building a boat I'll station some warriors and archers who will kill off sneaky mobs for me. I'm also toying with the idea of using the Steamheim Airships mod, but it seems a bit "techy" given the Viking theme. Maybe after I've played for a few more weeks, just for fun.