In vanilla freelancer, the Hogosha prevail upon the Kusari governemnt not to open doors for the Junkers. So they have no bases for example in Kusari. The Hogosha fill the same role as real life Yakuza and much as Junkers do in Liberty. But in Kusari (and modeled after modern day Yakuza) the designers let the Hogosha function more as "a part" of the society rather than as a seperate society merely tolerated (like the Junkers). Junkers are gypsies--an itenerant poulation tolerated so long as they do not trouble things to much. The Hogosha are the same scoially but have a place within the culture and have always been part of it and have had a past reputation (by analogy only looking at the Yakuza) as being somewhat contributory . So while Hogosha might be looked down on--they are still Kusari, part of tradition and history so it is unthinkable that they would be purged or criminalized by the government.
In Disco, the story has evolved through player response to where the Kusari government is more isolationist and the Junkers have become accepted as a real threat to Kusari. They are the "boogie man". They are the prostitues and drug pushers you don't want in your neighborhood. That has become the Kusari perception of them. In the current mod, disdain of things non-Kusari and concern for tradition and culture has scapegoated Junkers and hence the current ban.
In a straight vanilla freelancer it would not be the case but freelancer marginilized the Hogosha and Junkers (example: neither are in the SP story line). Kusari could have become more toerant but Disco play has directed it toward isolationism. Just as valid.