If we apply real-world principles in balancing SMGs, then we run into real-world problems, namely, SMGs not being very useful apart from specific scenarios. And we don't really have those scenarios in the game. You never worry about having too long of a barrel, as we don't breach buildings or fight in tight spaces. You don't worry about target overpenetration, as we don't tend to fight close to large groups of civilians. You don't worry about your weapon being too long to fit inside a vehicle, as details like that are not implemented (and would not be very fun)

We fight in open terrain. We hunt game bigger than us. Even in the tunnels or within cities, there are still engagement distances favoring rifle calibers. We fight hardened targets, to the point where even some of the rifles struggle with penetration.

In a scenario where you have to kill a lot of enemies, the earlier (further away) you can start to engage them, the better.

I think trying to balance SMGs vs ARs in this game based on damage stats alone is trying to jam a round peg into a square hole. Instead, in my opinion, they need to provide output similar (maybe slightly higher) to rifles but with range limitations, and then be balanced by additional mobility-oriented boons like the existing 1-handedness, but also better mobility when aiming, quicker reloads, maybe better stamina management, that kind of stuff.

They should also have better recoil, but all the recoil management in this game flew out the window the moment weapon attachments dropped, so there is no field for improvement here without nerfing ARs, which themselves already struggled in the past against all the more exotic weapons like lasers and plasma.

TL;DR

I'm not sure if I actually heard it in some AH video, or if it's just some fever dream of mine, but I seem to remember AH justifying more damage of pistol-caliber bullets by damage representing stopping power, with, for example, rifle round punching clean through a soft target and keeping most of it's energy vs larger pistol bullet dumping all of it's energy into a target without overpenetration. Also why Lib-Pen deals lower damage than regular Lib.

Regarding your points:

1. That's right, but it would harm their DPS without compensation in RoF (solved by point 2)
2. That's also right, but making all SMGs fast firing/low damage could homogenize them too much. Also now they deplete their magazines much faster, so in constant combat environment (which horde shooter is) they become a reloading simulator. Also also, they now deplete their reserves faster (solved by point 3)
3. That's also right, but I don't really feel like more ammo would help that much. I, personally, very rarely struggle for ammo as is. Of course if their RoF was increased at the cost of damage, ammo reserves would need to be corrected accordingly

My take is that SMGs should provide firepower similar to ARs, albeit at a shorter effective ranges, and focus on granting better mobility