When Wikidata links to a file in Wikimedia Commons, Special:WhatLinksHere on Commons currently does not display the usage. For example, Wikidata Lexeme:L99-F1 links to Wikimedia Commons File:De-Luftballons.ogg but the Wikidata page is not listed on Special:WhatLinksHere/File:De-Luftballons.ogg. Displaying such reverse links would be useful for maintenance.
Hm... in the sidebar on Wikimedia Commons (see screenshot), would it perhaps make sense to replace the link to Special:WhatLinksHere by a link to Special:GlobalUsage? Currently, there seems to be a usability/UX issue: the feature is already implemented (thanks for the kind explanation on this bug, I had no idea!). However, people may might never come across the Special:GlobalUsage unless they already know that it exists. Hence the suggestion to remove “What links here” from the sidebar and replace it by “Global usage” which seems to be a superset. (There’s a risk of cluttering the user experience when the sidebar has too many links).
Another potential solution for the discoverability issue might be to place a prominent banner (or header, etc.) on Special:WhatLinksHere, warning people that the displayed content is only within inside the same project. The explanation text could point people to Special:GlobalUsage.