If I'm not mistaken, I believe CX picks up passengers at YVR for its JFK-YVR-HKG service. By having the stop, CX is not only able to carry a full passenger load but also cargo revenue. Therefore, if CX is to consider flying non-stop JFK-HKG, the revenue upside from passenger only operation would have to be greater than the loss of full passenger and cargo revenue of operating the stop in YVR.

At the end of the day, it's all about the revenue.

Personally, I would rather have a short stop in-between. Even when I fly in the front, I prefer to be able to walk on solid ground once every 12 hours or so.