While I realize that 9mm NATO is standard in NATO and pretty much everywhere that armies are still buying new handguns, I don't think that is necessarily a good reason not to use something else if it's better, such as
.45 auto, for instance. And I think there are two reasons.
First, submachine guns are no longer commonly used by most armies. They have pretty much become more specialized weapons now that intermediate cartridge firearms are in widespread use. I'm not sure what specialized use calls for a submachine gun but that's pretty much the way things have worked out. Anyway, there is no longer a requirement that the handgun and the submachine gun have a common cartridge, although many armies somehow managed well enough for a while with two (or more) handgun cartridges.
Second, given that now a handgun cartridge is only going to be used in handguns, the ammunition requirements for handgun use in any unit is going to drop to very, very low. Therefore, there's hardly ever going to any need for resupply from allied forces, which really does happen with other munitions. The basic load for the .45 auto during WWII was only 21 rounds per person (on the person) and according to army staff manuals, very little was expended in combat, although the numbers quoted are averages.