How not show in a View certain taxonomy items if there are no associated nodes?
Easiest way is to add a relationship in the view to the node type that contains the taxonomy term reference field and make it mandatory. This will force Views to only return the taxonomy terms that are present on a node.


Edit your view
Expand "advanced" (if its not already expanded)
Click "Add" beside Relationships
Click "Taxonomy term: Representative node"
Click "Require this relationship"
Click "Apply"


Note: I used the representative node vs the content with term option for performance reasons, the former only retrieves a single node for each term vs matching every term to every node