Holy fucking shit dude. Press Ctrl + I in the game and stack that empire tree. Or just click the corresponding button in the top left of the HUD on the right of the Search button.

To answer your question:

Each time the pirates clear a planet, the remaining ships that survived the sweep of the gravity well will return to their Pirate Base (the one present in the system where the raid took place). Since you were continually being attacked by the pirates the AI players probably sent the pirates on missions to attack you, which explains why you were being attacked in so many different gravity wells.

The more succesful raids take place, the harder it becomes in the end to wipe out the pirate base. If you would select all the pirate ships in the Pirate base gravity well you would most likely see a huge amount of different fleets in the upper section of your empire tree. Each fleet represents a succesful raid.

the ai can also hire the pirates for missions and such so that could be it as well

It never ceases to amaze me the issues some people have with pirates, I love the rain of xp as the silly pirates fall from the sky.

On a more serious note it takes a balanced fleet to attack a pirate base or titan with attending fleet if necessary. As far as them attacking your planets well sometimes there is nothing that can be done about that in which case the best response is to destroy any planet marauders and leave the gravity well once the pirates have destroyed everything in the gravity well they will leave and you will be free to go back without having lost the planet or even having received any damage to it since you took out the planet attackers.

Also if you are far enough along in the game you should have sbases up in which case you can completely nullify any pirate attack. This is because pirates always go for ships before structures so you can take a small fleet and kite the pirates around your star base. Nobody ever accused pirates of being smart you just have to understand how to deal with them.