It's important to keep track of the scale of the damage. At typical velocities, one destroys about 1.7oz of tissue, the other about 1.1oz of tissue. It becomes very clear how important it is to put the bullet in the right place. Destroying an extra half ounce of non-essential tissue won't make any practical difference at all.
Right, given equal penetration, you can't expect double damage without double area (bullet diameter) and so as John KSa noted. After all, the .45 acp is only about 1.6 times large (frontal area cross section) than 9mm.
With that said, the amount of tissue destroyed may not be as relevant as the amount of tissue damaged. You don't have to destroy an artery to cause severe bleeding, but simply lacerate it. A laceration will actually destroy very little tissue, but can seriously compromise the function of the vessel.
As noted, destroying (or lacerating) non-essential tissue won't make any practical difference.