Its my understanding that some of these 9mm bullets went completely though the bank robbers from one side and stopped in the shoulder of the other side of the body on the way out.

These shots would have been fatal, though they didn' t kill the perp right away. A .45 certainly woul dhave punched a bigegr hole and might have stopped them sooner, but by no means would out penetrate a 9mm.
If you use good quality expanding bullets, the stopping power of a 9mm is virtually the same as that of a .45, and no, stopping power is not the same thing as recoil.