In reality it is a time consuming process which takes a lot of work. Basically for safety it was pretty much only done in good weather during the day while the sub was stopped on the surface. IIRC In order to submerge during the loading operation required the operation to be completely abandoned and the torpedo would be lost overboard if it was not yet below decks.
The amount of time required to move external reserves in SH3 i think depends on how many people you have in the torpedo rooms... load the torpedo rooms packed with movers and the job will probably go smoother and faster. but im not sure... it might default to a one hour operation just to simulate the difficulty of hoisting a toprpedo and positioning it into the angled hatch.
For ultimate realism: here is what i do... surface the sub and come to a complete stop at about sunrise. if the weather is such that the deck gun and flack guns cannot be used you must skip loading external reserves... however, if the weather is such that you CAN use the deck gun or AA guns then proceed with the loading of the torpedoes. Do not move the sub or submerge until the loading operation is complete.
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