I've never attacked the pirate base, but from the number of pirate ships there it looks like it would be hard to conquer. Do you get anything for taking the pirate base? Once defeated do they disappear for good or pop up again later?
Pirate bases can badly damage a trio of, say, level 6 capital ships, but yous simply pull them back when they get damaged, then come back once they repair. Or you just send in more capital ships or send in an actual fleet. The bases are surprisingly easy to defeat once you have gotten a few capital ships, and make for good experience.
I personally like the pirates, but think they should be changed in a few ways. First, there should be a capital ship of some kind in the severe attacks; either a Pirate-type Kol, or some ship unique to pirate raids, and they would be level 4 at least. Pirate bases should also have at least one capital ship.
Also, the bounty on yourself should impact your relations with pirates. If you have minimal to no bounty, pirates shouldn't bother attacking, as long as they are simply large-scale bounty hunters. Trade ships and military should also affect relations.
One thing I think would be really cool would be being able to hire mercenaries to either defend a player, attack a player, or raid a player's trade and refinery ships. Those mercenaries would have the same symbol as the player who hired them, but half of their symbol would be white to help distinguish them. Their ships would look like pirates, but would have blue, red, or yellow lighting rather than green lighting to distinguish mercenaries.