The ballistic difference between 9 mm and 40 Smith & Wesson out of the short-barreled gun is basically insignificant.
What is significant to me is the increased recoil and flash of the 40 over the 9 mm which makes it more difficult to shoot fast and accurately. As well the 9 mm gives you one more round capacity (+15%) which can be more important because of the lack of difference in ballistics.
Having owned, carried and shot Keltec 40's and a .357 Sig, Kahr 40's, and a S&W 642 .357 Mag as compact guns, I can say without reservation for me 9 mm shoots better in a small lightweight gun.
Capacity and shootability trump any perceived ballistic advantage. Science does not support the perception that one can shoot a small, lightweight .40 better than the same gun in 9 MM. Personal perception can be different than science though, just not for me.
Get the 9. You'll do fine.