For most freighters, the stern is naturally heavy. For that small coastal freighter, aim for engine room or further front. Tanker suffers most from engine room, quite a bit of open space in the bow and beneath the bridge as well. Rawalpindi is quite vulnerable to hit to the fuelbunkers (just in front of bridge in the hull).
Some general guidelines, but ultimately you'll have to learn from experience.
Not much I can do for the small coastal merchant, even if the rear hold and stern are completely floaded, and with the zones tweaked for 5-6 times more weight, it still floats. Just too much bouyancy in the rest of it.
To be honest though, the aim is for the possibility to sink it with 1, which is quite possible as long as you don't hit at the stern.