I understand why troops cannot go through ships that are still afloat, but I think things should be changed so that a destroyed ship is fully sunken, and that troops should be able to sail through where it once sat, like any other destroyed building. Right now sky raiders can fly over it once it's destroyed, but why not fully sink it and let us row through the flotsam? Ships are currently utilized as an indestructible wall in many popular base designs, and while this is an important creative element, I feel like a change to this would do good for the overall variety of designs in the game. Before being destroyed, things would function as they did before, letting the ship be a giant floating wall, which wouldn't completely invalidate current designs, but as soon as you managed to destroy it, it would open up a new path. Forcing players to either put more effort into defending it or rely on it less would hopefully encourage people to come up with more new designs again. Since this would clearly make things even easier for the attacker, other defenses would need various buffs to compensate (hopefully swinging towards less reliance on the GP while we're at it), but that would only further encourage players to vary their designs.
They do sometimes, its very buggy and certainly needs to be looked into. If I wasn't so lazy I'd capture a replay of that and post a better bug report on that.