DOSH.
There is a LOT of 9mm ammo in the world, and it's spread pretty evenly. Lots of places to find some 9mm.
There's also a good amount of 5.45 in the world, but it's more likely to be packed away in bulk in particular places.
Today, on the worldwide market, 5.45 is a little cheaper than 9mm.
In KF2's post apocalyptic market, though, 5.45 might be be much less consistently available, so the trader might charge much more for it.
(if KF2's AK12 is chambered in 5.56, the same argument still applies, but to a lesser extent)
For gameplay balancing reasons, the gun will also likely be cheaper. Maybe even a free spawn bonus, for moderately high level players.
Also maybe
more ammo carried, due to compactness.
These aren't 9mm and 5.45, but they're mags for very similarly sized rounds, so it demonstrates the idea.
Also 32rd mags instead of 30rd. In game the difference might be even more, and the commando perk bonus will likely amplify the difference.
Also likely lower recoil
Also likely lower weight gun
Also some people prefer iron sights
Also quieter