The pirates, in my opinion, should be like mercenaries that you can hire. Say you want them to attack an enemy's trade routes. The ships would be unmarked, so the enemy couldn't attack the pirate planet directly. So the enemy would be forced to protect the transports or just leave the transports to die.
incredibly good idea.
I also think instead of blowing up trade routes, pirates should instead steal, which is what they do best. After a pirate boards a trade ship, they steal all of the goods and stuff. After they leave, your trade routes income drops back down to what it was origanally, because traders are afraid of investing into something that will likely get stolen.
They might even conquer the planet and make it a pirate haven.
I think pirates should just start with a planet they use as a secret layer. You wouldn't be able to tell it apart from any other planet. And pirate ships will go there to hide, so that your fleets are left clueless when trying to chase them down.
It should happen due to the low morale of a planet and the planet's angry pop would fill the transports.
that's more of a rebellion than a pirateer, plus it wouldn't be that good of an idea, because your planets morale would shoot up to 100% (because all the mad people left), and you can just blow the ship up once it leaves the planet.