Why do cargo aircraft still have floors?
Because the overwhelming amount of cargo is fairly small and floors allow easy loading of both decks at the same time which is more important than the ability to load big cargo on occasion. By having floors you can load standard cargo containers quickly and efficiently. It also gives you the ability to standardize the containers with a reasonable degree of reuse most importantly they can fit into the lower deck of a passenger aircraft with out modification. Passenger airlines make a lot of money moving commercial cargo.   

When it comes to flying around big, cumbersome cargo there are simply aircraft designed and built for such a task like the Airbus Beluga



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