...And let's clarify that this "covering up" is due to the fact that the muzzles of the torp tubes are separate plastic bits that need to be glued onto the smooth forward ends of the torpedo deck pieces, but were left out in the construction of both the photographic model and the yellow desktop model.
So we aren't really talking about Starfleet in-universe installing shutters on a launcher type lifted directly from the Constitution
refit, but about Starfleet possibly completely removing such launchers and plating over the holes, or possibly installing new and more compact launchers that have hinged cover plates. Canonically, the muzzle bits were never there, but Sternbach's own art shows them in place - so I'd like to think Starfleet removed the Constitution
style tubes at some point after the 23rd century and installed all-new weapons in roughly the same location, with single tubes that we can see in the form of those tubular greeblies atop the top launcher deck and below the bottom one.