Factory ammo, or reloads? I ask because if you reload, you have some control over your powder burn rates which can affect velocities depending on barrel length. You won't see significant increases with slower powder and longer barrels, but you can squeeze a little more out of it. Velocity gains in longer barrels are limited mainly because of overall total powder capacity; even slower powders will get consumed relatively quickly. Ergo, chasing ultimate velocity means something along the lines of a 14" to 16" barrel. If you look at the "Velocity by the inch" link above, you'll notice a correlation across nearly every pistol caliber listed. 14" to 16" is the sweet spot for top velocity with the exception of 10mm and the +P loads. 10mm produces its best velocities at 18" because it has a higher powder capacity...so do the +P loads.
Pros for the longer barrel: top velocities...and pistol calibers arguably need all the FPS they can get for effectiveness.
Cons for the longer barrel: you lose all the advantages of a compact pistol build.
If you're going to build something with a 16" barrel, why would you choose a pistol caliber when something like 5.56 is going to be way more effective?
If I were to build one in 45 ACP, I would go with an 8". In every load listed on that site, an 8" retains anywhere from 91% to 97% of the top velocity listed. If your upper can run +P loads, all the better.
Anyway, that's my pragmatic advice, but I will caveat that by saying, if you're building it for fun or a range toy, go crazy and do what looks fun. Even though I build my own from a utilitarian perspective, I certainly appreciate unique builds regardless of how useful or effective they may be. Shooting isn't always about how powerful or gut splattering a round is, sometimes, they're just fun to shoot.