Ah, hmm, that's a point I could see splitting out a few factions - such as the Charterist rebels - at some point, if it became gameplay-significant. I don't particularly want to split actual core pirates into subfactions based on type, since that very much feels like unnecessarily complicating things. In any case, not 100% set on anything here; will keep this in mind, but no promises.
(Basically, if I run into something that's enough of a pain to deal with and that locking rep solves (or if a related bug comes up), I'll probably do it. If I don't, I don't see a reason to go out of the way to do it.)
If Pirates had stuff (I cannot find in Open/Black markets) worth buying for joining them, I would think about it doing so. As they are, they are a bunch of losers who failed to break out and make it big. If I want to be a pirate in Starsector, I would join a major faction then beat up enemies. I get access to better goodies and get paid for acting like a pirate. If I get stuck with junk, I prefer to stay as a free agent (either to build my empire or destroy everything) than join with other losers stuck with junk.
I'm finding Megas' statement making perfect sense: who would even BE a so-called pirate in first place?
If not secretly funded by someone, my answer is NO. NOONE would ever be pirate on their own.
Take a look at modern piracy(physical, not cyber).
They are well-organized and probably have relationship with some kind of government or rebellions.
It's very much similar to modern privateer except noone is gonna claim responsibility to their done damage.
Take a look at revamped economy, players will somehow be able to reduce competitor's accessibility so player can win the trade war.
Privateer operations are not allowed unless two factions are at war, so there can be secretly funded armadas doing the nasty work.
Take a look at free port, I think Alex has not explained how the underground economy and crime will be handled in colony in detail?
I think it's a good chance combining these up, and again make things simplified but not ruin any fun.
Idea: remove general "pirate" from game. Change it into a hidden faction that is perfectly fine with fixed rep at -50.
General random piracy will be done by independent guys just like how it acts now in .81 in far-far-far away areas.
When a so-called "pirate" appears, it's secretly funded by a market's opponent to reduce accessibility of competitors.
It then perfectly explains how all the weapons and maybe even the blueprints get to those pirate stations: it's secretly funded.
It can be one part of the underground economy exercise: a raided colony's product and/or an intercepted trade fleet's goods will get more likely appearing in black market for a few months after such operation went successful.
I'm not sure how Alex will making the crime and underground activities in player's colony managing, but what I'm imagining is you'll need to spend some money to suppress crimes; or let loose and eventually your stability drop and organized crime appears. Players can also spend additional money to try "make friends" with mafia boss, take control of both light and dark side of your colony. Although it might cause somehow reduced stability since organized crime is prerequirement, you'll then be able to actually "fund them to set a pirate base" to reduce your competitors' accessibility without heavy reputation punishment. It's an option for player trying to act like a "very clever badass".
I'm not sure if it'll go over-complicated if making it possible to trace back to pirate's funder and ask for some kind of ransom or reparation, but under assumption of all pirates are funded by competitor, it's perfectly fine setting them at hostile (rep -50).
Edit:
I think I forgot about pirate distress calls? The already-existed independent scavenger can do the job.
As player can make real and fake distress calls, why can't everyone else do same?
Some greedy NPC might just do the same and try ambush you if they think they can take you; or they pretend they pressed the wrong button and give you some fuel/supply in return for the false call if they eventually find you too big to fight against.