Yep, they came, must've been a hundred fleets on my meager medium-sized map. By their fifth turn every ship and starbase was gone, and I had managed to kill only two pirate fleets with my now gone military. Being a rather distant third behind the all-powerful Thalans and Altarians, I saw it as a chance to level the playing field.
But why stop there? After a few of my best ships were eaten up instantly, I realized that I could not fight the pirates- and I didn't need to. With literally dozens of pirate fleets "protecting" my borders and other militaries crushed, I needed not worry about building ships- at all. So while the AI builds ship after ship to get instantly vaporized, I build Terraforming and Industrial Sectors with military spending on 0%, building up my planets for when the pirates finally die down.
So when the pirates come and no one can beat them, just think about it- you don't have to! They are all the protection you'll need for a while.