I am traveling to Japan on Cathay Airlines. 5 hour layover in Hong Kong then on to Japan on Cathay Airlines. Will I have to go through Chines Customs even though I never leave the airport?
Even if you are leaving the airside (for example, for the food), you likely would not need a visa. Otherwise, you almost certainly don't need a visa.
If you are booked on a single flight (usually, you are if you're transferring from another CX flight or a Oneworld airline), then you don't have to leave the airside. If you are not, you will, but in either case you likely don't need a visa (judging from your name).
This answer assumes that you do not hold a Diplomatic or Official passport.
If you have booked your flight on a single ticket and you are not a national of one of the countries listed with a * or a ^ listed here you should be able to transit through Hong Kong without ever clearing customs. Furthermore, if you are not a national of a country listed with a #, you can exit airside into Hong Kong without needing to apply for a visa beforehand.