I’d take the Rifle Skill. Most Shotguns have at least a similar build as a normal Rifle (unless they have a rotary magazine or something like this), so that would work too. Smg’s might be a bit trickier, considering that they are more like something between a pistol and a rifle (form & size only of course).
I seem to remember that there are SMG holsters in the real world - bigger than a pistol holster, can take very big pistols, but smaller than a holster for rifles/shotguns. Maybe something would be a good idea, then you could put smaller smgs into the smg holster and bigger smgs in the XL holster with shotguns and rifles.