That's certainly a major problem, but the not the main reason. In the 1920's the Japanese made extensive gun test on the unfinished and scrapped battleships (Washington Naval Treaty). What they found was that shells that hits the water and passes under the main belt, penetrating the underwater protection can do extensive damage. So they modified their AP shells to be able to do this with more success and even their underwater protection. So their main tactic was to hit the water and penetrate the underwater protection, while reinforcing their own ships against this. if you think about it's kinda crazy that they made their whole plan around this, when they could not guarantee it would happen in real battle. So this is the answer. The Yamato's underwater protection wasn't made against torpedoes, it was made against AP shells, hence the thick armor. the Yamato class could withstand so much torpedo damage because of the sheer size of the ship, and buoyancy.
If you wish for, here is the source, but it's Hungarian....
http://acelmonstrum.host22.com/mus.html#5