Since WooCommerce 3.0 the catalog and search product visibility was moved to a taxonomy term for better performance.
Therefore you can exclude these products using the
Andvanced Options -> Exclude/Include results panel:
Drag the exclude-from-catalog and the exclude-from-search items to the right side, so products that are hidden from the catalog as well as from the search will be excluded.
Save the options, and it’s done.