Good questions. Not a 100% sure but looking at the items.xml for a18.4 it doesn't appear that there's any single shot damage difference between the two. And there's nothing special in the ammo9mmBulletBall entries for particular weapons.
Advantages the SMG has over the pistol, besides greater mag capacity;
MaxRange 65 vs 50
DamageFalloffRange 30 vs 18
(could be wrong but my understanding of the range bits is that there's full damage out to the DamageFalloffRange then it starts falling, until at MaxRange it's 0)
SMG is also a bit more accurate, and has slightly less recoil.
No idea if default RPM is effected by using the semi-auto mod. If I had to guess I'd say I think in single shot mode the SMG could fire faster than the Pistols 180 RPM?
Edit: hadn't caught that about the perk - burst bonus. I'll have to look into that; might be worth using a burst mod rather than full auto. Thanks.