I like where you're headed here. What if, it's never 100%? Let's say you can "launder" a ship. You can get fake registrations and have it altered in the general database. However, as you suggest, what if it only gets you 90% of the way. Let's say that last 10% is a main database that requires time to search, similar to the real life fingerprint database. That's why they don't run your prints at a traffic stop. Let's say that the only time this database is checked are major stops, ship sales, insurance applications, and a specialized scan.It should work like real life, you have a stolen ship and are always at risk of being "stopped" by police, yes you might have paid for legit tags or license plates to avoid 90% of trouble even if pulled over for a broken tail light. Then you break down and a "nice" police car stops to assist and looks a bit closer, maybe he knows the engine you have wasn't released the year on the plates, he looks at the VIN number and it doesn't match, busted, impounded, car gone.
Should work in anything that needs a deeper look at the ID of a car such as crashes, crimes, heists, security scans, restricted access to areas, background checks on you. Any of those should warrant the vehicle either attacked, you arrested or the ship seized.
Then you go pay the mega bucks and have the "jumping through hoops" to keep a ship, you can probably get a new VIN number but you have to get there first, you pay a fortune and I hope it takes a good while, no 20 minute wait, a week should be good especially on larger ships, you know they put ID in a lot of places these days, even in the glass of your side mirrors can have them.
I just hope if one day you do manage to attack, subdue and takeover an Idris that you need to get it out of there sharpish, if you manage it you're instantly wanted and need to get to a different system, no self respecting pirate would touch that damn thing so you have a cool off period where you hide it in a hangar for a while, then you can finally and carefully get it to the ID fraudster where you pay him a million UEC and leave the ship there for a week.
Finally you have something that can fool even a reasonably intelligent scanner system such as UEE jump points, patrols, landing bays on most station(I imagine) but not full on scrutiny.
You still have to be careful.
This would prevent the resale of a "hot" ship to an unsuspecting buyer. It would also stop the spread of stolen ships since they would mainly only be owned by the actual thief themselves. The in-game "grey" market would then be limited to those that knew they were buying a stolen ship. It would also provide long term risk to using a stolen ships, a level of risk that will never go away.
What if, they leave the door open for bounty hunters? Let's call them insurance recovery specialists. They get a reward for returning previously stolen ships. They have special access to researching this database. They can, with a longer scan, identify stolen ships and recover them for a reward. This would add to the bounty hunter game play. It would be a welcome addition since it looks like the profession will be a little sparse at the moment.