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Well, if the Free Captains are smart, and one would think that to survive this long against so many enemies, they must be... then Broken Rock may be a home port, but maybe only for temporary use. If you want to keep your home from being blasted, perhaps Broken Rock isn't a secret, but also home to a large civilian "non-pirate" population. In other words, perhaps they hide in "plain sight." Any attempt to 'atomize' Broken Rock would result in a cry of injustice the likes the Pact Worlds would have never seen in their lifetime (with so many civilian deaths for so few pirates).
I would also point out that the term "headquarters" is a rather loose definition for the Free Captains. After all, if each captain rules his own ship, it more like a confederacy (each 'ruler' having his/her own voice rather than a centralized governing body). Destroy the 'headquarters' and you won't really harm the powerbase since each captain is his/her own ruler anyway. You'd only eliminate one source of resources.
Worse, there's no guarantee of taking out the pirates since they mostly 'live' on their ships and only return to Broken Rock for supplies and the occasional meeting. And worse, Broken Rock is not the only port that does favorable trade with the Free Captains. So you'd have an uprising from several other locations still yet to be determined.
On top of that, the Vesk would not obliterate a civilian population no matter how many pirates they could eliminate. That wouldn't be honorable. And the Stewards, well, like the UN peacekeeping forces, they do condemn piracy, and they probably help fight piracy in specific locations (just like UN Resolution 2442), but to eliminate piracy completely is not within the scope of their power to do so (they don't have that many Stewards or resources at their disposal with everything else they do).
So as you can see, there's lots of reasons why Broken Rock still exists even if it is well-known.