Currently, deep category searches on Wikifunctions aren’t actually deep: for instance, deepcat:Contents only finds the nine direct members of Category:Contents. This should be fixed.

The reason is probably that the categories query service doesn’t seem to contain any data on Wikifunctions categories yet (example query) – indeed, the categories RDF dumps don’t even include wikifunctions yet. (This, in turn, seems to be because wikifunctionswiki isn’t included in the categories-rdf dblist yet.)