Bunks seem like the obvious way to store sleeping crewmen if the vessel is tall enough and you haven't developed hammocks, and even if you use them you'll need vertical space between them--not everybody can sleep at once.
Viking longboats had space on deck for the men if they took the sail down and tied it over them for a tent. Triremes, though--there wasn't a lot of room on those things. If they hauled in all the oars there might be room to lie down between benches, but probably this guy had the right idea: "Usually under blankets around their campfires on the beach." Non-warships would have more space--you could sleep lying on top of cargo, perhaps, and being taller in the water might make part of the deck available. Jonah was asleep in the hold. Coasters with short trips still have people crowding the decks to sleep however they can/dare.
Another rabbit-hole: what became of Viking longships? The Mediterranean ships were taller and stronger, making it hard/impossible to assault them from a longship, and aspects of that design were quickly adapted, making the classic longship obsolete.