You can use the following query for this:
SELECT * FROM Document WHERE dc:subjects/* IS NULL
Adding the usual filters on deleted documents or versions:
SELECT * FROM Document WHERE dc:subjects/* IS NULL AND ecm:mixinType != 'HiddenInNavigation' AND ecm:isCheckedInVersion = 0 AND ecm:currentLifeCycleState != 'deleted'
If the question is about the User Interface and the default forms displayed by Nuxeo (in the FacetedSearch for example), then you must override the search or add you own (Content-View in Studio, with the "Faceted Search" box checked), because by default, Nuxeo handles the empty parameters of these layouts as if they where not filled at all.
