You can't really neglect momentum sepecially at those speeds. Think of being shot like a colision because thats what it is. Momentum is what moves the bullet thru the object being shot (in our discussion a person). It is what gets the bullet into the person so the energy can do the destructive damage. Your talking about the kinetic enery of the bullet being the powerful force in this well the formula for Kinetic Energy is KE=1/2MV^2 and momentum is P=MV so if you say that you can neglect momentum because the bullets have very little mass then by that logic you could also neglect the Kinetic Energy of the bullet. When dealing with objects at high speeds you NEVER neglect the mass of an object.
Sorry, I didn't mean to give the impression that we need to neglect momentum as far as bullet travel goes. The DIFFERENCE in momentum in a .45ACP and a 9mm can be neglected, depending on which loads you are talking about and ASSUMING they both have enough to reach optimal penetration. I'm not saying that a bullet doesn't have momentum or that we can neglect mass when finding momentum, that doesn't make any sense at all. But as far as expansion goes, it is the energy that matters most. The reason why the kinetic energy of a 9mm is close to that of a .45ACP is because velocity is squared in the kinetic energy formula, meaning it is more important in getting larger values. If you don't believe me, do the math!