Suou's rifle might have dented the hull, but it wouldn't have punctured it. 25mm (.985 in), the penetration of the PTRD she uses, was enough to penetrate light tanks in the early part of WWII, but couldn't get through the later models.

A submarine's hull is thicker than that (especially one about as long as that one), and the high yield strength steel would take the hit better too. Most submarines can survive a near miss from an explosion. Suou's rifle wouldn't do a lot, even though they've depicted her shooting through stone already.