Internal storage missing: Nexus 7 16G down to 5.8G TOTAL
I had the same problem as OP flashing to 4.4.3 on a Nexus 7 16GB (2012).  My total storage as reported by the storage module of the settings app was like 6GB and running df from BusyBox/adb was reporting the same.  This is clearly a partition table problem and not hidden files or anything else.  I think that the problem was caused by several failed/aborted flashes that I did.  I was able to fix it by reflashing from adb.

In other words, I downloaded the latest image, decompressed it, and ran the flash_all.sh script.  (Of course after running adb reboot-bootloader).

For the record, I did NOT have to change the commands to fastboot format X.  

It would be nice to understand this problem better but for the time being, going from ~6GB to >13GB of usable space is quite a relief.