The 45ACP became the caliber of choice because it had considerable stopping power, when most calibers around 0.35" fail.
The 45ACP remained the caliber of choice because it WORKED, and the right people were in charge and they didn't give a damn about what NATO liked.
The 45ACP remains in use by elite units because it offers much more reliable stopping power, the use of suppressors has nothing to do with it. Elite units MUST stop their opponents quickly and surely, with as few shots as possible, because of their mission and the fact that they rely on swift application of overwhelming force.
You talk about penetration. The only thing the 9MM penetrates better than 45ACP is helmets. Got any idea how few soldiers can actually MAKE head shots in combat conditions? Got any idea how much better a 230 grain 45ACP bullet penetrates flesh, clothing, and breaks bone? Got any idea how much difference 115 grains of weight and 0.100" of diameter makes in stopping power and damage done, when you're dealing with bullets that do not expand?
The answers to your questions are:
Who cares?
Who cares?
Popularity and expedience.