The CX nonstop service between JFK and HKG is operated by a special A343, with reduced seating capacity and probably some limitations on cargo payload; CX is doing this in order to compete with UA and CO, with their nonstop flights, as they do not want to loose market share, especially with full fare and premium pax who choose nonstop flights whenever possible (business people especially want to get to their destinations and return as quickly as possible, time is money!)
The YYZ service, with a "standard" A343, and lots of cargo, has a little problem with the range, especially during certain seasons due to winds, etc. That is why the stop is scheduled. When CX gets longer range variants of the A340, look for the stop to be eliminated as they would also prefer to offer nonstop service between the cities - YYZ/HKG is an important market for business travellers as well.
As stated above, CX owns the "shorter-range" variants of the 777 and uses them primarily on regional flights where lots of capacity is needed.