If the one boat blew up the other boat, would Joker blow up the remaining boat?

He says he's a man of his word and so no.

He definitely would have let the other boat live. Either way, think of the chaos it would have created. If the prisoners survived, the people on shore would have rioted and stormed the boat when it arrived, since this group of convicts just killed a boat full of innocent people, and the guards lets them. And if the other boat survived, they would forever be tortured by the choice they made, and if they were no worse than the men they killed.