It's no problem to take the CX one-stop service from JFK-HKG... for the purposes of your ticket, YVR won't be a ticketed stopover...
Also, if you change your mind, you could even try to book the nonstop... it doesn't require a re-issue, becasue, again, your ticket will be valid for either service.
Although personally I've only ever taken this flight as a trans-con, never as a trans-pac, I do remember reading here that indeed the HKG passengers MUST get off the plane (but don't have access to the new CX lounge), or so...
But of course, this is for a different direction than you're intersed in... Eastbound, I have no idea.
Anyone?