What is DEYO?
Traveller Adventure offers us an example of a megacorporation altering a transponder on the player's ship so it appears to be owned by another megacorporation. Clearly both legitimate and illegitimate changes are available to the "right" people, so the danger you describe could be real: someone beats word of their naughtiness to a planet and adopts a new identity - legally or by crooked means. One could oblige a ship to wait in port a couple weeks while they were checked out, but time is money and companies will object.
On the "ripple" model, news of that change is going to go out - and eventually be received by folk who are hunting for the ship under its old name. They'll respond with an objection and an alert - which will likewise ripple outward, with a good chance that the ship under its new name will land someplace and then be queried about its new name and its old history. And, of course, the hunters will just begin hunting under the new name, this time with a record of the name change so they can formally tie the newly named ship to the old ship history. And if that ship tries to run a new name change soon after a recent name change, they're likely to draw some questions.