they aren't the size of ships, but they ARE the ships(reborn like girls so to speak).
I think they actually must be the size of ships, just hear me out. For their designs to make sense in a strategic setting, the guns and weapons are going to have to be capable of performing the typical duties of a destroyer, or cruiser, or whatever. There's no way they would be capable of bombarding shore emplacements if their main guns aren't actually large enough and powerful enough to do so- and the main turrets of the largest battleships were bigger than a house. It just makes the most sense. Of course this is human ship-girls fighting monster ship girls, so it doesn't really make too much sense to begin with, but I like to think that at the very least the naval capabilities of a military are going to reflect typical naval duties.
