As far as I have experienced with GWX, one torpedo hit at standard depth (4.5) under the first mast or in the most forward part of an merchant ship tends to sink it 85% of the time. Somewhat the forward compartments tend to flood quicker and waves reach the decks sooner. It may not sink if the sea is too calm but then you can use the gun to take it down with 5-7 shells. In convoy situations, always fire two torpedos to ensure a sinking.

This is a common behaviour in GWX 1.00. In the latest versions 1.01, 1.02 and 1.03 this behaviour has been minimised to avoid ships without bow to sink every time. In the later versions of GWX you need to aim your torpedoes to particular areas of the ship to have a chance of one shot kill.