The Yamato is a hard ship to sink, can take 8-12 torps depending on mods. Try to spread damage along the ship. Also, given enough time ships repair damage like your sub, but it can take them awhile.
As Donna said if it's in shallow water it may hit bottom, but the deck is above, so since you can flood it out to sink you must sink it by damage points which can take a few more torps, but you can sink it in shallow water. Regardless, try hitting underneath the turrents and engine rooms
I have yet to encounter or hunt the Yamato yet, my goal is to finish this 100K ton patrol, do another war patrol on the Pike and maybe if I can transfer to a 6/4 boat I will go hunt her down, but I do imagine that if you hit her with your fore tubes and she doesn't sink, it takes about 2 hours for a good reload team to load up 4 tubes.