I think, irrespective of old / new vehicle, useless for Customs department, smuggled vehicles, etc., the main thing, or their process of suspecting and confiscating a vehicle is, when the vehicle's record is not found in Customs record, their ledgers, WEBOC System ( https://www.weboc.gov.pk ), etc. and lastly, with Excise Departments too.
If a vehicle is registered in the Excise Department, there can still be a possibility that its record is not available in Customs Department, and such vehicle can also be confiscated (such cases have been there, and yahan bohat kuj hota hai, but let's leave this topic / discussion for some other time).
For Customs Department, any vehicle whose record is not found in their system, is suspicious and prone to confiscation, irrespective old / new, or even registered, etc. They confiscate it and then auction it. Money obtained via auctioning is the property of Govt. of Pakistan.
The vehicles which finally get auctioned are free from any legalities.
Once, it happened, and I personally witnessed it, that a Corolla car was up for auction, but just at the time of auctioning / bidding, some stay order, or similar sort of notice came, and it was not auctioned. It was pulled off.