I have the same set up with an early Service model and the 9mm barrel out shoots the 40 S&W barrel by a considerable margin. The only " negative" is that some brands of factory ammo do not push the slide back far enough to engage the slide stop after the last round. This is particularly true if a new recoil spring is being used. It becomes a little less noticeable after a couple thousand rounds but it will still happen. Remington/UMC seems to be the most frequent culprit but it has happened with Fiocchi, Winchester, Federal, CCI, S&B, and probably a couple other lower cost lines of ammo.
I have not had the same happen with a conversion barrel in an M&P yet but I have less than 100 rounds through it so far and have not gone through a number of brands. It is also getting close to spring replacement so I would not be surprised if a failure to lock the slide back occurs with a new spring.