What you are probably referring to are hatch gratings. All big ships had to be loaded with a lot of stuff, whether it was cargo or simply stores for the voyage. That was lifted from the dock , either by a dockyard crane or by tackle slung from one of the ship's yards, then dropped down through the hatch. When the weather was good, the hatch gratings provided ventilation below deck and kept sailors from falling down into what would be large, gaping holes. When the weather was bad those gratings could have canvas tied down over them. That canvas could be stiffened with battens, nailed down ( ergo "batten down the hatches" ) or the gratings could even be replaced by solid hatch boards, and canvas tied down over those as well.