The compliance rate for the 1968 Shelby registry (SAAC) is about 40% at the most. You know that after 39 years, they'd have most of them "corralled" by now, since it's always been a very popular car.
At the moment, the GT/CS Registry is at about 29% compliance, or about 1200 cars. For about every one registered, there is another one not (yet) registered.
There is a number out there, that is between "natural attrition" of regular '68 Mustangs, and Shelbys. That number is probably where the GT/CS is.
By looking at the stastics of other simular, late 60's registries of all cars, you can get a good idea where we stand.
I think to say that "half are gone" is pretty fair. My best educated guess is 2500 (incl. HCS) tops. There are the clones to consider, too, that can skew the numbers. Some of these clones are made from parts of "real" GT/CS cars that were damaged, salvaged, etc., over the years. You can't have 2000 GT/CS cars just "dissappear" over 40 years without those parts ending up somewhere....
The book will have a closer estimate. I can say that the west coast has preserved this Mustang marque, just by the original marketing nature of the car.
Paul N.