You can see on the pictures that the ship is very narrow in the middle (that becomes the stairwell/elevator shaft for going down into the undersea researchy are

You can see on the pictures that the ship is very narrow in the middle (that becomes the stairwell/elevator shaft for going down into the undersea researchy areas), so when it stands on end, the waves cause relatively small changes in the buoyancy. The big forepeak that provides reserve buoyancy so the thing doesn't sink outright if a big wave hits it, sits well above the water surface.