Tricky situation.. Zoners are sometimes getting killed by pirates just like Junkers are sometimes killed by lawfulls. Im not sure how often that is, but it happens... Anyway. Another part of the coin, lets talk about Junkers. They arent criminals, they're just.. weird.
In the RP sense Junkers also maintain neutrality just like Zoners do. The diffrence is that the Junkers are very carefull on contraband (while Zoners dont run it), they barely get caught and uncaught is not a thief. Although everyone knows that Junkers are smuggling, which makes Junkers sort of friendly with pirates, they also trade with pirates, making them deal with them fair. Black market etc. The most important thing is that Junkers make a neutral ground for pirates to land and they certainly need it, because they cant land on house systems for shopping. However Junkers tend to make good reputation among houses too. They scrap fields looking for equipment, even though this is only cover, taking scrap metal to melting facilities, doing favour for the houses. (according to Junker NPC in Texas). Also they occasionaly sell out Rouges or other minor criminals (according another NPC in New York), making the status with houses all the better. Another point is that Junkers bribe both Police and Pirates that helps them to improve relationships and maintain stability.
Police know but their hands are tied, pirates have to bare and so the neutrality remains.