No, it has always been thus at JFK. The G/A when I was based there had a 1,000 foot stop height because of the conflicting traffic above. We are talking about 30 years ago in my case and I suspect that it has been so ever since.
So, any professional aviator heading for JFK simply MUST include in the let-down brief that the G/A restriction is a measly 1,000 ft.
Believe me, if you are flying a DC-10 then you need to think ahead. Hitting the TOGA button would probably be a very bad idea!
Prior Planning Prevents Piss Poor Performance.