It would be interesting if pirates were more tied into the black market.

The pirates would have a default amount of resources coming in. Since their money and resources gains are limited, black market prices would go up and down based on how much they have. (longer lasting trends than what currently happens) It would encourage players to place their own supplies on the market. Also allows for strategic draining of the market. If pirates were disabled, the market would work like it does now.

Pirates would primarily gain by sending out small fleets from their bases to destroy things, gaining a small amout of resources per ship kill. They would seek out trade routes and congregate in neutral gravity wells, since destroying trade and refinery ships would be better. Because of this, you'd have to monitor neutral wells around your territory.

Raids would only activate(start the countdown timer) at certain bounty thresholds. If they had lots of money, lots of bounty would need to be in play before they attacked, if they were near bankrupt, they would launch for anything. The severity would depend on the bounty involved.(It seems to depend on empire wealth as it is)

To avoid losing most of their fleet on their way to the planet, their base would have a stolen Kotsura Cannon or a similar device that allowed them to send a raid fleet on a one way trip directly to a planet (bonus if it disables the defenses/strike craft for a little while too, to allow at least a little initial damage.) If the pirates destroyed all the structures in a well, they would move on, returning to base once the money hit 0. In this way they could store up extra ships for a later raid (up to a maximum fleet supply) 

I think that like this, pirates could become more of a concern without just buffing them. The market would depend on their actions and they would actively seek to take your resources. Taking them out would mean you had access to less resources, but letting them form pirate controlled areas in your territory might be bad for your culture rates, although if they worked as a demi-faction you could make deals with them to let them work semi peacefully with you. (bounty would still trigger raids.)

Other ideas regarding pirate crafts

• Their siege frigates, instead of destroying planets could steal a bit of money from your empire every time they hit a planet, since there's no reason for them to kill planets. Following the idea though, scuttling things like space stations and planets could help lower the bounty on you.

• There could be a construction craft that is used to constuct things, such as spawning their gauss cannons in neutral fields they occupied.  It could also just build some sort of space station that could steal from resource collectors in the well, regardless of who owned them, or act as an underground trade port that recieved money from any trade ships passing by. The space station could also lower the culture of adjacent planets and/or give a chance for them to spawn neutral armadas. Basically something extra to look out for in the neutral wells.
  

• There could be a raid leader ship that stole the income from a planet while it was in the well (making it's output to you 0 or similarly low, vs the siege ships actually taking money away and negatively affecting your income.)  It would probably have more defensive weapons.