There are many, many great end-game combos of nano plugins. It took me hours, but I listed all of them right here :

Combo 1 :

• Iron Curtain - reduces incoming damage by 30% (can stack up to 90%)
  
• Iron Curtain
  
• Iron Curtain

Combo 2 :
--No other viable combos

To put it simply, let's say for my birthay, I can choose between a game, another game, or a computer to run them. Regardless what I pick, I can't use anything if I don't have the computer anyways.
In that case, the computer is the triple Iron Curtain, and the games are all the other nanos.

This has to do with the current state of the game : The loop feature still requires many adjustments, the most important being enemy damage.

In first loops (~1 to 3), enemies aren't many, so the player is already bulky enough to be able to choose whatever nanos it needs.
From loop ~4, however, stages' enemy spawn cap gets concerning. They don't hurt more, but they are more to shoot ; and since the game is made to emphasis stealth by reducing enemies' accuracy when the player crouches/hides/doesn't move, that means it gets even more damage when it's moving.

I started running on full curtain from loop 4, and it was fine until [almost] the very end of loop 10. However, since 3 nanos equal a 90% damage reduction, removing a single one multiplies incoming damage by 4, which is already unplayable.

Highest loops are filled with many fast and bulky enemies, that respawn quick as well .
Thus, the current direction of the game forces the player to go for crowd-controlling weapons, that can do a lot of damage quickly to multiple enemies.

Rifles, pistols and shotguns, as cool as they can be, aren't really good at that, so most players will put them aside as soon as they get a "real" weapon.

The main stat boosts to aim for are DMG and MAG. Pierce doesn't matter because the only viable weapons all have this stat maxed already, and accuracy/fire rate don't neither since every weapon has to be shot at a reduced rate in order to consistently hit weak spots.

I chose DMG for obvious reasons, but MAG especially comes handy when enemies begin to come bulkier and in greater amount. Reloading does eat a lot of time, plus a high mag means more total ammo carriable (which isn't a problem for machineguns anyways).

Straight to the point, talking mid-late game (from loop ~4), there are only 3 weapons worth farming (excluding DLC) :

• HK-11
  The "late game starter". Its high base penetration/mag size makes it so it only needs a good bonus in DMG to be viable for the highest loops.
  Highest stats owned :
  -DMG : 175 (base : 20)
  -MAG : 442 (base : 100)
  
  
• M240B LMG
  A substitute to HK-11. Has twice its base power, but requires to be fired slower due to its low accuracy.
  Highest stats owned :
  -DMG : 365 (base : 40) --Seems like max damage is close to (base * 10)
  -MAG : 196 (base : 100) --Can likely go as high as HK-11
  
  
• Milkor Mk I --Since it's the first, why bothering to give it a number?
  The very meaning of "crowd control". Even though its base MAG is clearly not enough --My highest damage takes around 4 hits to kill normal enemies on highest loops --, it has an extreme mag bonus potential for some reason. I luckily got my hands on a boosted 43 MAG, which is absolutely huge, considering that the carriable ammo limit is only 12.
  It is also extremely powerful against armored enemies, such as Jena and some mine fighters. Unfortunately, Juno is immune to grenades, while it still backs off of them.
  Highest stats owned :
  -DMG : 366 (base : don't know lol)
  -MAG : 43 (base : 6)

As far as I know, machineguns drop from Juno/Jena, boss level exit crates, any mine exit crates and HQ crates (the ones that require currency).
I think Milkor only drops from Juno/Jena and HQ crates though.
Loop 10 loot doesn't seem to have higher stat cap than lower loops, so I don't think the difficulty matters, as long as it's legendary.

...Just felt like putting this here.
Grenades are irrelevant in late game, since Iron Curtain inevitably fill every nano slot. At best, they can scare enemies for a very short time, which can help a little on some missions.

Melee... looks like a forgotten feature. Last time I tried it, it dealt 6 damage, and stunned just like a dash... too bad it takes ~1.5 second to charge while enemies can kick back even quicker.
I don't remember ever using it seriously.

Here are a couple advanced tricks for those who want
(Ngl most of these were probably not intended by the dev...)

• The player runs faster diagonally than forward
  Probably gone in a couple patches
  
• In sister assist missions, those still alive at the end follow the player
  This is the best bait anyone could dream of, perfect if there's a generator / sister rescue mission next. --Who even manages to have sisters still alive on loop 10??
  
• Dashing while crouch-walking makes the character jump slightly
  Even though this isn't high, it's still enough to jump above some obstacles such as small crates and barriers. This can come in very handy in Gate Factory Entrance stage, to jump on the minecart from the crate aside, which allows to avoid any melee attack and focus on the mini-bosses.
  
• The heal charge bar doesn't reset if the player gets downed while charging a nanoheal (unless the key is released while downed)
  If well timed, one can let enemies lower its HP, then charge a nanoheal when it's about to die. If the heal was half charged when the player got downed, the full heal charge will start half full. Especially useful in mine crystal missions, but will likely be patched soon.
  
• The character doesn't interrupt reload when downed
  Using this along with the previous tip can save quite a couple seconds...

From my observations, it seems that enemies always aim by default at the position where the player's head would be while standing up.
As a result, the lower the player's head is from the ground, the more bullets it will dodge (pretty clever!).
Enemies also have some inaccuracy, which allows bullets to sometimes hit a crouched player (especially with these stupid shotguns).

Here are the different player positions, from safest to most dangerous

• Downed player : Very low, dodges pretty much all bullets
  
• Crouching stationary : Lowest "alive" state
  
• Crouch - walking : The head's a bit higher
  
• Crouch - running : Even higher, begins to eat quite some bullets
  
• Standing / stand-running : Not for long, dude

This stage is always the same and takes place only in one room.
Considering mine exit crates all drop rare weapons like HK11 and M240B MLG, this is a very nice place to farm.
The only interest of loop 10 precisely is its very high clear bonus for leaderboard (4000 * 110), for ~5 minutes of fighting. Definitely looks like the best place to farm top 1.

Mini-bosses' armor is a huge pain, but not for a DMG-boosted Milkor Mk 1 --Mine came so handy overall I named it "Mommy Milkor"

Try it.
On loop 10.
Once you'll see the FPS, you'll understand why I never finished it.
Once you'll reach the twins laser robots, you'll understand why I stopped trying.
--gg if you came that far tho

burp.