It happened to me several times when I attacked small to medium merchant. The ships just wouldn't go down, but I didn't want to wait for long so what I did was I surface the boat and finished the ship with deck gun.
For small-medium ships, whenever weather allows, I always use one torp and when they refuse to sink I finish them with deck gun.
OTOH, I have sunk large ships (large cargos and merchants) with only one torp. I fire two torps and after the first hit, the ship just sink.. waste the second one
