I hope we are not forced to connect Commons categories to Wikipedia categories because of that, which has been a nasty side effect of connecting things through Wikidata, due to misunderstanding the Gallery space in Commons and taking it for some kind of equivalent to articles, which it is not in the least.
But a huge lot of Commons categories probably should never have any Wikidata item (ex: "Eiffel Tower taken from the west corner of the Trocadero terrace" (don't know if this one exists, but that's the kind of stuff we usually create there to classify views), so I'm not especially confident that should be done.
Best,
Paulo