From Expedition to Zhodane: "His [the professor/owner of the planetoid ship] initial efforts brought him to the attention of the University of Cipango and the University of Cronor, both within the Zhodani Consulate. He developed friendships with various sociologists there, sharing findings and data with them as time and itineraries permitted. Ultimately, these acquaintances enabled him to receive permission to begin a long-term investigation of society on Zeycude."
An alternate way to interpret the ship's uncanny ability to evade detection is to declare that Rock is an anthropologist's blind, intended to hide the ship from civilian eyes but not from the security grid*, allowing the Professor to enter and exit Zhodani society (aboard Pebble, and with the tacit cooperation of the local starport authorities, while Rock drifts in stellar orbit some reasonable distance from the primary world) while appearing as a local. The Zhodani navy, system defenses, and starport authorities at a high level have been ordered to cooperate with the University program and ignore the ship, treating it as a natural (and plotted) asteroid. When they see it powered down, they assume it is in a parking orbit while the Professor is doing his bit planetside.
As the adventure notes later, "The local Zhodani have noted that he is aware of ship and troop movements and other details in the vicinity of Zeycude. Monitoring his surface thoughts, they have detected a simple curiosity about the movements, and he has been detained as a protective measure. ..." With that low level of detention, word that the ship was no longer to be ignored has either not gotten out to everyone or has gotten out as a low priority advisory, instructing them to treat the ship as they would any regular merchantman or civilian ship, so the ship only occasionally attracts attention and - if powered down - they again assume that the occupants are planetside and that no one's aboard, especially if a life scan shows no life signs.
*Exactly why a sociological researcher moving around in Zhodani society would need a disguised ship in the first place, or why a Zhodani university would entertain a sociological research proposal in which a disguised ship flitted through Zhodani space, or why the Zhodani Navy - which assuredly would have been briefed on such a plan, if only to avoid unfortunate incidents - agreed to permit this absurdity is beyond me. It was a problem in the original, it remains a problem. Best I can offer is that for all the press about them, the Zhodani strike me as frequently naive and insufficiently paranoid where Imperial matters are concerned. I suspect that is an artifact of their psionic culture - it's hard for them to think like sociopaths.