It's NOT worth backtracking to 1.2 over, there are far too many improvements in 1.3.
If this is a showstopper for you, find taihosan maru in the Roster/Japan/Sea/ folder and delete it (make a backup someplace).
Of course any mission that explicitly calls for that ship will then CTD
I don;t think there are any.
Again, this also seems RARE in cases with the stock game. As far as I can tell it is related to damage to the front of the ship, and it has to be pretty severe. If you must attack one, don't put 4 fish in it, heheh.
tater