In T157676 the first iteration of categories in RDF in the graph engine is being build. A nice addition would include if a category is hidden. On Commons we have normal "topic" categories that are not hidden like https://commons.wikimedia.org/wiki/Category:Haarlem and tracking categories for all sorts of things like https://commons.wikimedia.org/wiki/Category:Images_from_the_Rijksdienst_voor_het_Cultureel_Erfgoed or https://commons.wikimedia.org/wiki/Category:CC-BY-SA-4.0 . In a lot of cases when querying the category tree, for example when filtering out overcategorization ( T110833 ), being able to filter out these hidden categories is needed.
A lot of the other wiki's use hidden categories in a similar way. The hidden status of a category is already stored in a page_prop so some code can probably be re-used there (Wikibase page_props end up in RDF already).