[BUGFIX] Detect missing files in empty storage

Improve the check for missing files by properly treating
the case when a storage is empty.

Change-Id: I8fba9be2622a4cd742c0065b68a8daf77f8a484a
Resolves: #54414
Releases: 6.3, 6.2
Reviewed-on: https://review.typo3.org/31427
Reviewed-by: Frans Saris
Tested-by: Frans Saris