I always assumed that the Joker had secretly swapped the detonators (i.e., you push the button, and the ship you're on is the one that goes).
This would fail to create the hysteria he was looking when the ship that didn't detonate the bomb also didn't explode. The hysteria he wants comes from getting people to actually commit things they wouldn't normally do.
hmmm...make it so that when one of the two ships hit the detonator, both explode?
wow. Amazing analysis on the situation, very interesting comparison of the situation to the prisoners dilemma game. Excellent read!
I love the conclusion:
However, I think this calls for a new villian in the third movie of the trilogy: The Game Theorist. Much like the riddler, but deadlier and requiring Batman to use mathematics to fight crime.