Ya know, the openings may be a simple case of what worked best for the skipper. If the skipper was a bomber pilot, then his emphasis would have been getting bombers in the air and loaded up as quickly as possible. Whereas a normal surface sailor skipper wouldn't really care that much.
So it's possible that as the ships entered the yards, the skipper may have said "hey, those gallery storage spaces are cool! Could I have ten more each side?" Or, alternatively, a skipper could have said "all they did was cause flood damage from the elements: seal up all but four on each side." Skippers were like that...
When you watch "Fighting Lady" onboard Y'Town you see the skipper and airgroup commanders going through great pains to get all planes bombed up belowdecks in the hanger prior to raids. Other skippers may have opted for loading topside.