The one in-universe criterion would be that these tubes should be as difficult for the crew to access in-flight as possible, to hide their true nature. This might indeed best be achieved by having 72 individual single-shot launchers that come pre-loaded (or at least starbase-loaded-by-stevedores-in-black) and don't requite any in-flight tampering such as loading of the next round...
They definitely weren't pre-loaded. The tubes had to be loaded one at a time by a crane when the ship was in firing position. Seems the torpedoes themselves were actually stored in the cargo/shuttle bays close to the launch tubes, which were themselves in fairly awkward positions hardly appropriate for weapons stations.
On the other hand, these were supposedly refitted in a somewhat hasty and clandestine manner...
Hasty, yes, but not clandestine. Everyone on the ship knew what was going on, and everyone was noticeably uncomfortable with the implications. Most of all Scotty, who DID in fact question Starfleet's collective sanity and ultimately resigned in protest.
I'm going to see the movie in 3D again tonight so I'll let you know if I notice anything new about the tubes.