Seriously though, your idea about the custom-ordered piercings sounds very believable. And speaking of The Fighting Lady, in the original book it is even more apparent that especially the first skipper - in Yorktown-II's case, Jocko Clark - could have a great deal of say-so on how the ship was fitted-out, prior to commissioning. Plus, the more I think about it, seems likely such openings could also easily be installed or plated over, as desired, during refit, as well.
In fact, up at Patriot's Point I was noticing exactly that; where the WWII-vintage hull-side openings - some of them very large - had simply been plated-in, with the weld lines clearly visible from up close.
All in all, pretty good news for the modeler, and the possibility for using "artistic license" to use your own best guesses of which and where these openings look most realistic...
When are you going to grace us with another carrier, Donny - been a long time, hasn't it?