This very question presented itself to me numerous time when i first started playing SH3 and I was getting frustrated emptying half of my torps into just one ship.
The answer is that part of what determines how fast your target will sink is where your torps strike her and part depends on what kind of cargo she is transporting. You can sometimes sink a medium merchant with just one well-placed shot while that same ship may end up taking four torps to send to the bottom on a different encounter.
Depending on your target, you may want to target the boiler room, ammunition depot..etc. Many threads have been devoted to this very question
One thing you must remember is that multiple hits in the same spot do not increase damage, so if you have a ship that's refusing to go down make sure that your follow-up torps target different sections. (BTW I've heard a few Kaleuns warn me to avoid hitting diametrically opposed spots on a ship as this may flood the ship while keeping it balanced and thus negate any keeling over action:hmm
Hope this helps and Good Hunting!