I don't know about the law etc. Don't know whats right or wrong but I have discussed the issue with a Customs official, a car dealer and a lawyer. All of them, one way or the other, gave the final statement that the matter will keep on hanging like this for years and final verdict, whenever it comes, would be in favor of these car owners.
Customs official point of view: IHC has given the verdict that the scheme was illegal but FBR had the authority to introduce such a scheme on Govt's direction as per law (he showed me some official Customs book having laws and rules and regulations and also made me read few lines which honestly I didn't understand as law is not my field :S ). He then said that the present Govt, however, has amended the laws and we no longer have the authority to introduce any such scheme in the future. However amendment has been made by the present Govt and can't be applied to the previous Govt's actions. By the way I do remember reading the news in "Nawa-e-Waqt" regarding such an amendment and that FBR has no longer got the authority to introduce any such scheme in the future. So if the amnesty scheme was illegal then, then why the present Govt had to change the law?
Car Dealer's point of view: Many big fish have got the vehicles cleared under this scheme and they won't let these vehicles to be declared illegal. He didn't give me the names of the big fish. 
Lawyer's point of view: The said lawyer is my cousin and according to him the decision of the IHC judge falls under the term what he called as "Bad Judgement". He further said that the FBR most likely didn't present the case properly in the IHC. He had a lot of arguments which I won't go into details of 
In addition to that he also pointed out that the Balochistan assembly is already quite angry over the whole case so Govt and courts will be very careful.
In the end I'll just put forward my observation.
1st, The local manufacturers are the main reason behind the whole case. Amnesty scheme cars, although old and smuggles, still were a great threat to their sub-standard vehicles so they had to do something. Once these vehicles appeared in the market they had to so something fast and thus they put forward some one in the name of his love for the mother land.
Now although the LHC has issued the stay order and even if the scheme is declared completely legal later, enough harm has been done to the repute of these vehicles so these cars don't pose a threat to local manufacturers now. [I]Now they are going after the reduced duties on hybrid vehicles giving large sized ads in the newspapers.
[/I]2nd, if the whole thing goes illegal there would be a lot of mess. In the areas where people are legally allowed to keep NCP vehicles, (yes, there are tribal areas and agencies where NCP cars are registered and kept but they have to stay within limits of those tribal areas, I did see a lot of cars in Swat after crossing Khan Garh with number plates having written on top of them "NCP") there the people will simply want the refund of their taxes and won't hand over their cars as keeping NCP vehicles in those areas is officially allowed. This will give a good financial blow to the already money deprived hungry Govt.
3rd and the most important, those who have bought these vehicles, relax. Keep the vehicles for as long as u can :P, for those who are thinking of buying such a vehicle, stay away, and in the end my condolence and a moment of silence for those who bought the fleet of em for investment purpose and now stuck. (H)
