Yes. I would definitely take the cham out. If you have a removable tray, just take it into your bath tub, rinse with hot water. The spray on the vinegar solution, wipe down with a damp washcloth, then rinse in hot water again. Then towel dry. We use tgus for our guinea pig and ferret cages. It works!
Well it depends on what odor you are talking about? Some odors people talk about cleaning mean there is something medically wrong with your chameleon or something wrong cage. None of my chameleons cages really smell except damp and like plants, so for deep cleans it's all about removing spots and dirt that is hard to get up.