Most hatches were meant for cargo and were quite large. These would be secured by nailing them shut with battens and canvas. But any large ship needed to have uninterrupted access to the weather deck so that the crew members on watch could be relieved. And in a storm, most maneuvers and emergencies would require calling up the entire crew (or an entire watch) for additional manpower (reefing sail, bracing yards, securing damaged rigging). So they would always leave a smaller hatch or two open, unless the vessel was a small boat where the crew planned to remain on deck for the duration of the storm.

In this period all hatches were sensibly placed on the centerline of the vessel. Everyone expected to take on some water in rough weather, as the gunports were never perfectly waterproof, nor was the hull/decking itself.

Source: I could list several dozen books here that would probably contain evidence for the above common knowledge that is readily available through actual lived experience with extant replicas of 17-19th century vessels. Young Sea Officer's Sheet Anchor (probably) Seamanship in the Age of Sail