LAV Driver has it right. There are plenty of instances on record in which two-deckers weren't able to open the ports on their lower decks due to the weather.
Furthermore, there were plenty of reasons for opening gunports other than wanting to fire guns through them. Particularly on board a big fighting ship in a warm climate, the ports provided desperately-needed ventilation. And running the guns out significantly increased the amount of deck space.
Plenty of display conventions in ship modeling have little or nothing to do with literal, scale fidelity. Surely all of us admire the wonderful old English "Board Room" models, with their unplanked bottoms and, in many cases, their beautifully-executed rigging. But no real ship ever looked like that.
I have to disagree with Mr. Mondfelt on this one. In my opinion there are plenty of "legitimate" ways to exhibit a ship model. To my eye a ship-of-the-line with all the ports on one deck open and all those on another closed would look a little odd, but I firmly believe that sort of decision should be the preserve of the individual modeler.
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