Does a contract to build a deck need an occupancy clause?
To me it sounds like boilerplate contract talk. Normally, when you get a building permit and there is a final inspection on something and it passes you will then get an occupancy certificate. 

Can't say I've ever seen it for a deck, but depending on your municipality or whatever "authority having jurisdiction" requires, maybe you do need a certificate of occupancy before you can use it.

Ask your contractor about it and have them explain it to you. Don't sign something you are not comfortable with or don't understand.