It seems to me like the author of the article might mistake reloading torpedoes with refitting at port.
I couldn't find any more info on the whole process of reloading a torpedo so I did some other research.
First, there's this picture, which shows what's been written in the article (the floor being removed from decks). But it clearly shows refitting at port.
Then, as you can see from cut-away pictures, all torpedoes are stored right behind the torpedo tubes:
Then there's this picture:
You can also see here that all torpedo mounts are on rails so they can freely move left and right. But is there enough room for the system to select the right weapon mount?
Looking at those pictures it looks like they're mounted on 2 rails. That makes 10 mounts on each rail. Considering that each torpedo has 533mm in diameter, and they are stacked very closed to each other (like those supports in the last picture) that gives us about width of about 5.4 meters (with some safety margin). Now, the boat is about 10m wide. I don't know how thick the hull is, but let's just say that the thickness plus the fact that tubes are slightly below the widest point on the hull will leave us with 8m of space. I think that is enough room for at least two of some sort of temp compartments to store mounts that "gets in the way" of selected weapon. Or they are just removed from the rail (the last picture shows a gap between rails). So it seems that if the selected mount is the closest to the tube it just slides in. If not (for ex. the closest is Mk48 and you want a Harpoon) it takes longer, because all torps placed before the wanted mount need to be removed from the rail. Perhaps that thing might take a while , unless there is some automated system that can stored unwanted mounts for the time of reload. In any case, this shouldn't take hours like the article sugested.