Say you start out with 100 pilots. You have two options:

1. Send all 100 pilots to Japan with full fuel tanks. 25 make it back alive.
2. Send 50 pilots to Japan with twice as many bombs. 0 make it back, but 50 are still alive.

the military wants to recoup that cost by sending everyone they bother to train out on a certain number of missions.

No, the military just wants to accomplish its missions. If more pilots are alive after each mission, it means more pilots available for future missions.