On the argument about whether SMG's are more accurate than pistols, that is completely dependant on the weapon. The MP10 is more accurate then most, if not all pistols, but then you have the Micro Uzi on the other side of the scale, that is signifcantly less accurate. While I'll admit I'm not a weapons expert, My understanding is that most weapon types have exceptions and anomalies that makes blanket statements about accuracy between two types of guns without specifics somewhat moot. However, in a game you have a limited amount of time to add weapons and types, so reasonably Devs generally create types of weapons that follow a standard such as all pistols short to medium range, all shotguns short, etc.
In the case of Alpha Protocol, while if you do use an SMG it's dual wield, you have multiple weapon options, so you never have to do that if it doesn't fit with what kind of spy you created. For my first character, I'll probably end up going pistols and assault rifles, single suppressed shots to the head, and never get up close and messy, because that's how I like it.
That's my 2c anyways.