saying it has been closed at May 32rd, 2013 and will be demolished in 2015 and therefore it is no more part of the airport map with the airport's website:
Work on JFK V2 started many months before that so, it's fairly obvious we couldn't be fully updated with the real world situation when the scenery was released.
It's a general case of not always being able to follow every airport development. When O'Hare changed its runways, which is of course a way more important change than a few disabled parking spots, we released the update more than 1 year after the event, and we might have to do another update shortly. You just can't expect we'll always and constantly follow up every airport changes, especially when they are so small like this.
I'd say that, since the terminal will be demolished in 2015, it would be best to leave the parking spot active in the AFCAD, otherwise most users would believe there was some kind of problem, if they say the actual parking, without the ability to use it. If one is really disturbed by their existence, removing them from the AFCAD is really trivial.