Waterproofing LEGO bricks
I would try liquid latex (liquid frisket) which you can buy in most art supply store.

This will not damage the bricks and is easy to peel off. You can apply it using a cheap throwaway brush, either in between the bricks (like a cement wall) or as a thin transparent layer on the whole hull. I recommend the second method because it's fast, straight forward and the easiest one to clean up.

I use this stuff for all kind of painting and molding jobs. It's a great material.