Probably comparable to asking if a 69 shelby would affect the value of a 69 Boss 429. Just in modern times of course. The terminator cut its notch in the bloodline. No worries.
It really depends on what the final version of the Shelby turns out to be. I'm not a fan of the new bodystyle and many other 03/04 owners feel the same way. I think a lot of people were expecting the new Shelby to have a twin screw and were disappointed to learn it won't.
The dealers are certainly going to jack the price up beyond belief when they first come out. This might make some people on the fence decide to keep their Terminator.