iPad memory used if far higher than sum of all App's memory usage I've got two iPad Air, one 64GB the other 16GB. Both on iOS 7.1.2.

On my 64GB iPad, the sum of memory used by all Apps very closely matches the memory used figure above the list of Apps (40.3GB vs. 41.2GB). On the 16GB iPad, the sum of memory used by all Apps amounts to ~720MB but memory used is reported as 7GB. 

How do I find out what is using the ~6GB? It can't be iOS itself, is it? I guess, I would expect to see a ~6GB difference between the numbers on the 64GB iPad, too, if it was iOS.
When your iPad is connected to the computer, click on the Device and look at the bottom of the screen. There is a bar that shows how much data each category is using.  What is the size of the "other data" category?

Your iPad stores not only the Apps but there is a lot of stuff like:
Browser cache,
Mail cache,
Mail messages,
Mail attachments,
Safari's Reading List,
iTunes Backups,
Game data,
Saved data files,
Call history,
Notes,
Media,
Voice memos,
etc.

To see what is using the memory space on iPad: Settings->General->Usage

In this list: All installed Apps are listed, tap on any App to see the actual App size and the amount of documents and data used by this App.

To delete this data, you have to delete the App, restart your device (press and hold Home and Sleep until you see the Apple logo) and reinstall it from the AppStore.