I didn't stick around long enough to see if they sank from using flak guns. I do know that the deck gun will sink them. :D I've gotten 2 so far with the deck gun.... 35 tons each. And it's the last time I do that. I now avoid them no matter what's going on.

I have sunk about nine of them with the Flak, I would rather save the two shells for Merchants.:D
But taking them on at distance is the only advisable thing to do, because they can do some nasty damage to your hull, if your near them too long, so a keen eye is needed, for I use the Single Flak, so I don't waste too much Ammunition.

I think the best way to try to fix burning PT boat would be increasing its hitpoints. Fishing boat has 100 hp and PT boats have only 50, and never seen burning fishing boats, unless i had some business in it!

So I bet it would work, I read in another thread that ships could take little damage when spawning into the game.