Lanefan
Victoria Rules
The "advances" would no doubt consist of making heavier, thicker hulls - fine for defense but not much use for getting anywhere in light winds; and even more so if the ship is oar-powered rather than sail.Well I mean, it just seems like, if a creature can attack the hull of the ship where you can't get at it, and this happens often, then you'd expect shipbuilding to advance in some way to counter this problem.
Flying, yes; though a battery of roof-mounted ballistae can help there.Instead, it's just like how D&D worlds are littered with medieval castles that are completely useless against flying or burrowing monsters.
Burrowing can be dealt with fairly easily, at least in 1e, by having someone cast Forbiddance on the ground beneath the castle and extending its AoE down into the rock/earth below.