I load Cor-Bon +P 230gr HP's in my P12-45 for defense, and my favorite practice ammo is MagTech 230gr FMJ, which is rated at 835fps on the box. I've never Chorographed either of them, but the POI is close to the same for both at self-defense distances, and the MagTech is a lot cheaper to practice with, and it has yet to give me any problems. I would think a steady diet of +P ammo in any semiauto could potentially cause problems over time, but that depends on how much shooting you actually do. I do shoot the Cor-Bon occasionally just to keep the "feel" of it, but I see no reason to use it for target practice all the time. But, that's just me.
As far as the original question goes, the type of powder being used and its burn rate will dictate whether or not a shorter barrel is that much of disadvantage. The first thing you'd have to do is check to see the actual velocities you're getting from whichever ammo you're considering. Then, decide which bullet would perform "best" at it's given velocity, and go from there.