While I don't know of any explanation for the inability to block the cargo scanner. I can say that ships are picked up on ship sensors via their emissions on the electromagnetic spectrum. Things like infrared emissions from the ship's radiators can only be hidden by stopping all emission of infrared and visible light, which is what silent running does (which also disables shields because they too emit some form of electromagnetic radiation). And of course that's supposed to work on the AI, if they weren't currently bugged with the ability to pick up silent running ships at a normal range.