Higher velocities and modern JHP pistol bullets really don't mix well. Some are going to over expand and penetrate less, some are going to fragment more (again less penetration), and some are going to expand okay, but have the petals fold back more along the bullet shank, and penetrate more deeply, but with less wound volume. You are right that velocity might be retained at longer range... but you may also be compromising short range performance. It's going to be very much dependent on what load you use.
The flatter trajectory is not going to matter that much inside 100 yards... and beyond that, it's really not going to matter. The slightly higher velocities from a SMG or rifle don't really effect trajectory that much... its still a fat non-aerodynamic low BC bullet (compared to rifle rounds) and its still damn slow (compared to rifle rounds). I'd be surprised if the difference in trajectory for the same round fired from a handgun vs a rifle or SMG was more than 3-5" inside 100 yards. Beyond that, you might as well lob 60mm mortar rounds.
If I was going to buy a PCC/SMG I'd probably stick with my same ammo choice that I use in my 9mm pistols right now: a modern 147 grain JHP. Its not going to gain as much velocity from the longer barrel, but the heavier bullets also retain velocity a bit farther out. I think they would stay in the effective window of velocity a bit better than the lighter options. In fact, I really really want to build a Glock mag fed 9mm AR with a 7-12" barrel and eventually put a can on it. Mostly for fun, but I could see it having uses for defense, within its known limitations.
What I am getting at, is that there is no magic 9mm SMG/rifle load that I know of. Anything SMG or rifle specific is going to probably compromise performance from a handgun, which IMHO defeats the purpose of having a pistol/SMG/rifle combo using the same ammo/mags.