NRT is not 24 hrs. airport. Arrival and departure between 11 p.m. and 6 a.m. is not permitted except for emergency and other unforeseen circumstances.
If the departure of NH 1009 from JFK was delayed by more than 2 hrs. (after 8:05 p.m. departure from JFK) then likely happen is that the departure from JFK will be delayed till 3:05 a.m. or later next morning so that the flight will arrive at NRT after 6 a.m. local time.