No worse than the vertical intermix shaft (depending on which diagram you use) of the refit from TMP through TSFS passing right through the center of the torpedo launcher and topped off with a nice glowing dome.
Actually, It passes between the photon bays, not the launcher's themselves. THe launchers are only a small forward section of the bay. But I was looking, where are all the 94 photon torpedoes on the Enterprise-A stored? (Yes I counted scotty's inventory on screen. There were 94 photon torpedoes listed on his display in STVI). I mean you got that big loader on Wrath of Khan, but where are the Torpedoes stored? Oh and Did anyone else notice that the torpedo bay on the Enterprise was not as tall as the set used in wrath of khan?
I am one of the people who likes to think of this JJprise as being relativly the same size of the original (People at ILM are dumb, give Bernd Schneider some credit, he really thinks these things through, and gives perfectly logical explanations, people just dont want to pay attention to what he says). The Windows and Hatches would all be way out of size for a 700 meter vessel. -so In conclusion, it all comes down to this. Starfleet vessels got Harry Potter Magic space expanders. Like the one that allows Voyager to hold 17 shuttles. (and allows the Delta flyer which is bigger than the shuttlebay doors, to fly out of VOyagers shuttle bay). Lets not forget in Nemesis Riker being on the Enterprise E's non existant deck 29, and almost falls down at least 15 more non existant decks in the Ent-E's own pit of doom.
I guess what I am trying to say here, Star Trek has always had issues with Infinite stuff fitting in Finite space.