Interesting idea! I like the way it works now, but it sure has some potential for optimization.
I really like the neutral extractors and would appreciate more diversity for neutral structures. So how about neutral tradeports, frigate factories and research stations? Located in grav wells without a colonizable planet. All these 'freelance' structures could belong to pirates initially. Players can capture them thus competing with the pirates and each other.
The neutral structures would have to be very valuable creating the goal to defend them. The extractors now don't really matter in mid- or late-game, right. But what if neutral frigate factories would allow players to build pirate ships equivalent to the units that would otherwise have to be researched by the players? Or special research in neutral labs? Here comes a nice use for starbases in the Entrenchment expansion
Problems: Strong pirates in the beginning (because they start into the game with this 'empire' of capturable structures) might be a problem.
Your idea of pirates scouting around for targets is also cool. And having them getting stronger if the black market is used extensively is also nice. Though they would stomp me every game