The time in the sub must have been fun - after all, what (structurally) are Starships if not "subs in space"?
Anyway, back to the thread- the shelves do indeed appear shallower, I hadn't noticed that! Sometimes the filming angle can play tricks but in this case it's a pretty clear departure from the plans. I would suspect that the change was made because the original design would leave next to no space for stagehands to move between the walls. McCoy's shelves differ somewhat in appearance too - maybe someone on the production team just happened to have a suitable set hanging around they used them instead?