To greatly expand the variety of NPCs without taking up too much more data, I propose NPCs that randomly have alterations. These unique versions could have increased difficulty in many regards, through higher stats (more hull, shields, defense, attack, or cloak) or even new abilities that the normal versions do not possess. In reward, the NPC could have higher XP, higher chances of stronger loot dropping, or may even drop completely different items! Here is an example:

Suspicious Dark Warper:
The Dark Smuggler's Guild operate directly within the black market, dealing in illegal goods. Dark Warpers sometimes ferry expensive merchandise between anonymous parties. They carry few weapons, but are difficult to hit. Though this one looks a bit weighed down with cargo...

"Suspicious"
NPC types: can be added to any common NPC
Increased difficulty: higher cloak, gains "panic" ability that greatly raises attack but lowers defense a little
Increased reward: drops a few mineral points and artifact points when defeated

this could be cool... but other than making npcs harder or easier and getting some credits whats the point? are specific artifact drops more common? or do they have a chance to drop rare artifacts? or new artifacts? anyway, +1 for the idea!

Yeah, I like the idea, adds a little more variety to them and has a lot of room for expansion.

big +1 to this... even if this was only applied to the less liked ones like flamehawks and warpers. maybe a 1/10 chance to be Suspicious.

To clarify, I mentioned So I have two other prefixes that could describe this:

"Heavily Armed"
NPC types: can be added to any NPC that can reward modules
Increased difficulty: higher attack, gains "confidence" ability that slightly raises attack and defense
Increased reward: NPC is more likely to drop higher-tier modules, less likely to drop non-module rewards

"Irradiated"
NPC types: can be added to any NPC
Increased difficulty: higher attack and shields, gains "magnetic cancellation" that lowers player's defense
Increased reward: NPC gains additional drop. The extra drop may be one Shield Amplifier, EMP Sphere, or Quantum Flare.

I like this idea. Here's some more potentials:

"Command"
NPC types: uncommon or rarer
Increased difficulty: gains "Command" ability that calls in other NPC's on your battle tab to engage you at the same, significantly increasing the damage you take as you have to defend against multiple enemies at a time.
Increased reward: Significant increase in XP reward.

"Spawn"
NPC types: rare or rarer
Increased difficulty: gains "Spawn" ability, spawning extra, weaker NPC's on the battle tab.
Increased reward: Additional NPC targets appear on battle tab beyond normal amount. Once killed, the battle tab returns to normal amount of NPC's.
Note: could potentially combine/merge with Command Ability.

"Plague Ship"
NPC types: can be added to any NPC
Increased difficulty: gains "Epidemic" ability that infects players ship crew with a disease, randomly reducing attack and/or defence and/or research output for a random amount of time. Also affects raiding and raiding defence. (Since these are crew-based too)
Increased reward: NPC gains additional drop. The extra drop may be Stryll Pathogen or Mutagenic Cartridges.

"Engineer"
NPC types: can be added to any NPC
Increased difficulty: gains "Repair" ability that, once damaged, allows the NPC to repair it's shields and/or hull.
Increased reward: NPC gains additional drop. The extra drop may be Repair Nanodrones or Shield Restorers.

"Pirate"
NPC types: can be added to any NPC
Increased difficulty: gains increased cloak and attack, reducing chances of critical hits against it and increasing damage taken by players.
Increased reward: NPC gains additional drop. May include a large cache of Minerals or Artifacts.

"Explorer"
NPC types: uncommon or rarer
Increased difficulty: gains increased scan, increasing chances of critical hits.
Increased reward: Reveals the location of a random planet.

"Armed To the Teeth"
NPC types: common only
Increased difficulty: significantly increases attack, but significantly decreases defence.
Increased reward: NPC gains additional drop. May include Ancient Crystal Foci, Crimson Obelisk, or Crimson Amplifier.