The way I'd like to see multiple pirates done is with a gang system. Basically, each pirate group in the game is a gang and they have access to their own blueprint set. Over time, and with successful raiding, those gangs gain power and new ship blueprints to make them more powerful. If the player takes out their bases, then that pirate gang is destroyed. New gangs spring up from mercenaries/scavengers going pirate, deserters leaving major factions, and desperate civilians leaving unstable markets with converted ships.
Even better would be if gangs actually kept track of their ships. So they have an initial set of ships that will gradually gain D-mods and get destroyed over time, while also adding other ships based on their ill gotten gains from trading with the black market, from commissions, and captured enemies. If powerful enough, only then does a gang establish a base. At that stage, underworld contacts could also have a gang that they're either associated with or have dealings with.
Let's say we have a Tri-Tach deserter, who goes on to raid the Persean League and get a Hegemony Commission. Eventually his fleet is an s-moded Aurora he started with, leading a few captured PL carriers and midline ships, escorted by pirate and Hegemony auxiliary frigates. If this guy establishes a base, his raids and patrols would have access to some PL schematics that the player could potentially get their hands on by raiding or maybe even doing missions and/or buying.