First off, big bad shooting at the same spot on a ship. Good Kaleuns know you should shoot at different places on a ship when firing a salvo or successive shots.
I play the vanilla game too...for now, and I agree sinking a T3 with a single shot is pretty rare. BTW I'm in May '42 in my first career.
The only time I've sunk a T3 with a single shot was with an accoustic homer, dead astern at about 450 metres. Totally blind shot as the bugger slipped away in heavy fog. My jaw dropped (this is probably the part I like best about the game, those "moments" when you see something new or unexpected).
I think most times it takes two fish, both from close range (400 - 900 metres), the first set to magnetic one metre below the keel, and the second set for impact at a depth of five - six metres. I suck so shooting at the middle of the ship will have to do.
Still the early electric fish work best for me, and other than that one hail Mary, the acoustic homing ones have up to now been iffy in performance. But some T3s take as many as three fish, and man those awful, long lingering deaths. But if you have the patience and if you can knock out its rudder or props, you can always shadow it until fair weather arrives and deliver the coup de gras with your gun. Guaranteed way to sink a T3 with a single fish!
From the little of the game I know, I'm not sure merchants are upgraded with respect to armour or health/hitpoints. Guess it wouldn't be too hard to snoop in the game files to find out. Of course they do get guns as you've probably found out to your discomfort, but many of the T3 I've encountered don't have guns.
Well, I hope I confused the matter even more. :P