Because LIberty is full of Liberal Capitalists, and they prefer money from fines and enemies shot than strict rules being followed and government intervention on private business.
Because indies don't represent the faction as a whole. JM also has good-ish ties with Liberty, so they wouldn't be quick to remove us. Congress was almost booted, but for some reason at the last minute they got to stay.
Honestly, Junker indies make me very sad sometimes because they don't take the role of a Junker seriously.
Repeating above, poor players (indies, though not always) dont represent the faction as a whole. RP-wise, the Junkers arent all smuggliers or pirate-helpers.
Think of it this way: there's a business in the real world. For demonstration purposes, this business will be an industrial material importer in the U.S. This business has dozens, or hundreds, of shipping freighters bringing material from overseas to distribute into the country. These materials are legal - they're things like steel beams or industrial lubricants or motor parts or whatever.
Now, every once in a while, one of these ship captains will take a 'side job' to bring illegal drugs or weapons or immigrants or even terrorists into the country, hidden among their otherwise legal cargo. If one of these particular vessels gets caught by the coast guard or similar agencies, that one captain might be imprisoned or fined or even barred from the country, and the business may get some flak, but overall it was one incident among hundreds of normal deliveries, and the decision was up to the captain rather than the company, so the rest of the business doesnt get any real action levered against them.
That's the junkers. Now, add on to that the fact that most liberty police are corrupt and can be easily bribed (due to the fact that they're a corporation rather than a government-sponsored entity), and the fact that military groups like the Air force or navy (LSF/Liberty navy in this case) dont really care about one small-time smuggler and have bigger things to worry about, and there's no reason for the country to ban the business as a whole on the actions of one individual.
Well I suppose that after all that time thay'd start figuring out that there's something not right with Junkers and start infiltrating them with LSF agents or something. Also they be mad about vigilantes but have a whole goddamn smuggling ring under their nose.