Hogosha are quasi-legal in the game and therefore many traders and other players from other Houses will indeed be red to them. All Houses are not the same but they have similarities and the Junkers and Hogosha share those similarities, such as being quasi-legal entities that are often red to other players. They both have very shady dealings and therefore do not need to bring undue attention to themselves. A base firing on innocent traders would bring such attention to them.
The very fact that base defenses can literally rip through transports and other big ships rather quickly should disbar their use as defense platforms in major arteries of trade between houses. This could be sorted out by moving the base a couple clicks away from the Planet?