Per a conversation I had with Bader on Discord:
If hierarchies are supported, it makes sense for all nodes to show up in Unlinked References, if the purpose of Unlinked References is to catch places where you, for whatever reason, didn’t explicitly link.
For example, if in your daily journal you quickly wrote: “* made the best chocolate cake today” and forgot to link it, it would show up under “recipes/chocolate cake” as an unlinked reference.
Another example might be [[humans/jane]], where in this page I would expect to see an Unlinked Reference to a block that says “went dancing in the streets with jane today.”
Presently, it shows up only for the first node in the hierarchy (humans, in the above example).