Not sure about them all, but back right after the game first released several people found the Sen Toku class boats tied up to a few docks and were unable to make them sink. The subs are only modeled for ports so it's entirely possible that they were never enabled to sink in the game.
I do recall that in Grey Wolves for SH3, they were able to add in AI boats, but could not make them change depth. They either ran surfaced the entire time and could not submerge, or ran submerged the entire time and could not surface. I expect it's a game limitation rather than a mod issue.
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We, the unwilling, led by the unknowing, are doing the impossible for the ungrateful. We have done so much, for so long, with so little, that we are now qualified to do anything with nothing.
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