From Kentico perspective, there is no such tool, since it would be too performance heavy (even our notice on missing database file representation is killing azure storage).
Automation for this would also be a bit complicated. Media file usage will be spread in web parts, document fields, widgets and even transformations or templates. This would require you to crawl over CMS_Document and other respective tables and look for file GUID, or name... Since this data is in XML mostly you would need either custom SQL script to search through larger portion of DB, or C# parser for XML to find out whether file is being mentioned somewhere.
It is doable, but it would take some effort and it will certainly be quite resource consuming.