If she flooded that fast & from multiple open hatches, she probably wouldn’t have crushed. This sub was crushed. If the sinking occured in the manner described, I’m betting she was still buttoned up with decks awash. The shot tookout the periscope & flooding the control room below the sail. They probably failed to control the flooding or control the dive given where they were hit.
One of the pictures shows at least on periscope intact. A hit on the conning tower could have had the same effect though. It might even explain why the tower did not implode. The rest of the boat would have been buttoned up, hatches between compartments closed, etc. Still the open hatch is the one leading to the ammunition stores for the deck gun. perhaps the boat did flood through that hatch, but it was the only one open, rather than a bunch of hatches being open. That early in the war, and against a Maru rather than a warship, I’d think they would have only been using the main deck gun, and perhaps a machine gun or automatic cannon (20 mm most likely) on the bridge, the latter to suppress the gun crews, if any, on the Maru.