Unlike real life, SR5 rifles (both assault and sniper) are very viable in CQB where shotguns, pistols, machine pistols and sub machine guns should excel. When on a shadowrun (and being caught inside the secret research lab will not really be any worse if getting caught with an illegal firearm) it make little or no sense to use a shotgun or a SMG when the other options include assault rifles and sniper rifles... progressive recoil or not.
Actually, there are plenty of reasons to use a shotgun or SMG in close quarters. Sure, if all you look at are damage codes, they seem inferior, but when you look beyond that, there's many apparent reasons.
Shotguns - While shot rounds might not do as much damage as your sniper rifle, they can be very good for dealing with grouped enemies, or in subduing enemies, since they're more likely to do stun damage. A shotgun with gel rounds is also damn good at subduing enemies. An Enfield AS-7 with SnS rounds is nasty, as well. A shotgun also works off the same skill as sniper rifles, so it makes for a nice close-in weapon.
SMGs - CONCEALABILITY. Can't stress this enough. An SMG can be easily hidden under even a normal coat, making it much easier to get around town without drawing the attention of the Knights wherever you go. In situations where you care less about "Kill everything dead", and more about "Keep their heads down so I can get away", an SMG is always a worthy choice.
But really, the biggest argument for using these in close combat goes back to the same thing discussed in another thread. Police see you with a pistol, they'll bring out the shotgun. You have an SMG, they bring an assault rifle. And so on. Assault rifles and sniper rifles gets HTR teams on your 20 ASAP. And that's when you get to be on the receiving end of sniper fire, or people mixing flash-bangs and automatic weapons, and the like.