That's correct on the YVR - JFK flight on CX: you will not pre-clear due to the arrival time. The US preclearance area is closed for the night when that flight lands.
You will have to deplane, sit in a holding area at the gate, where you will have to go through another security check at the gate, and security must clear the plane again.
Then you'll reboard and then they'll let the people who get on at YVR board.
Then you clear at JFK first thing in the morning, which can take a while unless you can get off the plane super early and walk fassssst to customs.