Don't forget our second meeting with the ex-pilot from the WC4 intro. He didn't get recruited into the BL, nor is he back in Confed. We can only assume that the pirates we had met earlier in the game were in many cases pilots like him, recruited by Tolwyn's folks into various proxy organisations, given equipment, and then cut loose with some basic instructions. The whole point for Tolwyn was to create a case for large-scale military intervention. Promoting piracy was very much a part of the package, because if all else failed and Confed refused to go to war outright against the BW, at the very least Tolwyn could then say that an intervention is needed because the BW are a failed state incapable of controlling their own space.
In short - the reason pirates are flying around in Thunderbolts circa 2673 is the same as the reason pirates were flying around in Talons circa 2669: because someone in Confed illegally sold or handed over surplus fighters, no questions asked.
The real question with regards to pirates concerns the silliness of their modus operandi as seen in both Privateer and WC4: blasting ships is not an effective way to get rich, even if you occasionally might be able to tractor in some cargo that survived destruction. Where are the boarding parties and stuff?