[Sailor Steve]

That was done partly because it was considered realistic and partly because it was a much-loved feature in Aces Of The Deep. No boat or ship is perfectly sealed, and they all leak. This is taken care of by pumping the water out, something you don't dare do while Silent Running. So in AOD if you were silent running, sooner or later the boat would start to sink and you'd get a message from your LI: "Cannot maintain depth without running pumps, Herr Kaleun!"

Since SH3 doesn't do that for silent running, NYGM's answer was to do it whenever you were at silent running speed, i.e. very slow. There is a mod that changes it. I'm looking but haven't found it yet.