I am told since it is a slug round (which is far more bullet like compared to other shotgun rounds and does not have its own damage model), design felt it best to use the SMG damage type to make it integrate better with the perk.
First thank you for taking the time to respond back. Nice to get info from the developers themselves. Secondly though the developers logic is very flawed here for all the following reasons:
1) Shotgun slugs ARE shotgun shells just like shotgun pellets are. Here's a pick of them side by side.
They're literally the same thing! A slug is just a giant pellet essentially.
2) A submachine gun by definition is a machine gun that uses handgun/pistol bullets. The Stunner is neither a machine gun nor does it use handgun/pistol bullets. Not even close.
3) Classifying the Stunner as a SMG because it fires a slug instead of pellets is as silly as saying a water balloon, a super soaker, a garden hose and a bucket of water don't do water damage. Instead a water balloon is more like a grenade, so it should do explosion damage. A super soaker looks like a assault rifle, so it should to assault round damage. A garden hose looks like something the firebug would use, so it should do fire damage. And the bucket of water is an up close attack, so it should do slashing damage. I'm sure many would agree the above logic is completely ridiculous.
4) Besides the HRG nailgun, there's the other 3 elephants in the room here which are the HRG Bastion and the G36C assault rifle. Both of which do assault rifle damage instead of SMG damage despite they're exclusive to the SWAT. Final one being the Stunner itself or in this case it's alt fire which does the same damage as a grenade launcher (ballistic + explosion) rather than SMG damage, and the primary fire should make sense too. So clearly weapon damage making sense to the design of the weapon trumps what class it belongs in.
5) Continuing the above argument about damage belong to class, if that's true then the VLAAD nailgun should be doing slashing damage instead of shotgun damage (I thought it did piercing damage, but it's a crossperk with the Support I guess) and the HRG Teslauncher should be doing slashing damage too. Instead that one does microwave damage and EMP damage. Speaking which...
6) Unrelated to the Stunner, but shouldn't the Ion Thruster do either microwave or EMP damage instead of slashing? Unstandable you don't want it to do fire damage since it will feel too much like a Firebug weapon, but microwave or EMP damage does make sense for that weapon. Plus it would make the Ion thruster a unique type of microwave or EMP weapon.
If the developers need something to make the shotgun slug different from shotgun pellets, there's already a difference: the Stunner's slug only does 80 damage vs shotgun pellets which often does over twice the amount of damage. There, that's it. Shotgun slugs are weaker than shotgun pellets, but make up their lack of power with more accuracy. That's all the developers need to seperate the two. No need to try and be more elaborate by putting them in completely different damage types.
Finally giving the HRG Stunner shotgun damage (as well as grenade launcher damage for it's alt fire) will effectively make it the SWAT's strongest per shot weapon, which the gun truly deserves and feels like should be a bigger heavy hitter weapon than a nailgun.
EDIT: I also remember something else very important here which is the Stunner also does shotgun penetration. Since it does 2 penetration which is the standard penetration for shotguns, but it doesn't do shotgun damage despite firing shotgun shells? What kind of logic is that?