Most of the ships that bit it were second-rate (ie, battleships) anyway, and with the infrastructure still intact, Japan basically screwed up the one chance they had of keeping the Americans out of the pacific.
OOC: I realize that but it was still a disaster, that it could have been even worse doesn't mean it wasn't. Even a best case scenario doesn't save Japan as it is screwed no matter what. By the fall of 1943 the US breaks even in AC and planes. Considering that the US planes by that time were better it goes quickly downhill after that, if not before.