As soon as you make something one shot lethal, you remove any incentive to gear above that point, the lower you set that bar the less important gear becomes since the only real relevent metrics in this type of game are damage and survival (there are types of damage and such, but the point is that there isn't a lot of room for much else). Why do Shotguns and Sniper rifles need to exist if I can just headshot something with my basic assault rifle and kill it?
This dismisses any and all gear progression in non-loot shooters. The reason you'll still want sniper rifles and shotguns is the same reason we don't use assault rifles for all of our combat operations in the real world - different weapons are made to solve different problems, at different costs and complexity, with different levels of risk. The trick is to have game systems that present those problems and showcase and accentuate the differences between different pieces of gear that provide a solid balance between risk and reward. You see this with unlocks in games like COD and Battlefield and others, and you see it because those games have tried to develop their own long progression systems and player investment systems and light RPG elements
without scaling damage.
So you use a sniper rifle at long range but not in close quarters where a shotgun will easier and more effective, etc. Different sniper rifles could be distinguished by all kinds of properties: caliber and penetration, range, weight, capacity, mobility, recoil, rate of fire, reliability, particular options for attachments like scopes and suppressors, current condition (new, worn, busted), ease of use, ease of upgrades, ease of customizations. Those are some of your dimensions for loot. Instead of a level 1 item meaning a certain amount of DPS against level 1 enemies, it would represent a common, low tech weapon, or maybe a higher tech piece of kit but in a state of disrepair. Higher level items would be different classes of weapon that require more skill to use, or lower level weapons that have been modded and customized.
Its not like there can't be very real reasons to acquire and expand your arsenal besides the old standby of level based obsolescence, but it requires game systems that make those differences important. So you get mechanics like sway and breath control for marksman weapons like sniper rifles which can again play into other gear that can optimize these values, but at the cost of building a loadout that is very situational - ie. You aren't always going to be tackling enemies at long range where you have time to set up your shots. Sometimes you'll be in closed quarters with short sight-lines, sometimes you'll need silenced weapons, sometimes you'll want to avoid overpenetrating targets, sometimes you'll need anti-armor or anti-personnel, sometimes you'll want more stopping power than fire rate, etc etc etc. Thus you won't just want different classes of weapon, you'll want different types within each class, and even different customizations and tweaks for each type. And none of these considerations are exclusive to twitch shooters. You could model all of these factors in a turn based shooter like an X-Com and blend both RPG management with a more grounded logic behind the shooting.
So yeah, I still don't think you need level gating and damage scaling to have a reason to acquire loot. Eventually you'll have all the skills and all the weapons, and they'll be in mint condition with all the mods, but that would happen regardless of how you design the game.
That you are capable of taking down unarmored enemies with any firearm doesn't remove difficulty or progression. Some enemies can have higher levels of training, make better use of cover, push forward only when in groups and flank when players are suppressed. Some can have armor or shields, or attack with flashbangs or smoke, some will have weaponry better suited to the combat zone, some will fire and maneuver to force you to flush them out. Some will attack in larger numbers, from multiple directions or call in reinforcements. Don't throw all of these elements out there at level 1, mix it up as the setting calls for it, and ratchet up the complexity as you go, not just the health bars.
But I'm sure its a lot easier just go with the MMO/RPG standby of just having the damage numbers go up with each level, and end up with a situation where fighting a 2nd level enemy with 2nd level weapons is pretty much the same as fighting 20th level enemies with 20th level weapons, and the playerbase will excitedly wait for the next expansion where the numbers go up even more so they can work their way back to the new numeric status quo.
Its a Clancy game right? The numbers have never been the star of the show, the particular weapons and gear are, and the tactics they afford are. There are reasons to choose one model or another, one scope or another, and reducing that complexity to a simple calculation where one of them is +3 DPS and the other is +5 DPS does the license a disservice. Its as if The Crew was a Forza game, but with neither the physics nor the upgrades (The Crew flattens that all out into color coded +5 looty parts), and where your cars performance is limited by its parts, and those parts are limited by your player level. It wouldn't be strange to see Forza fans grumpy at the thought, and its not all that different here.
But hey, as long as they don't pull this kind of thing with Wildlands I'll be OK ;p