content type showing as link but not in "node_type" table
Found the resolution on drupal.org

One comment explains how to "reset" the content type from the navigation menu.


  This fixed the problem! What I did:



Go to the navigation page, admin/structure/menu/manage/navigation
find the link to the content type that is no longer there. It should be in the list under "add content".
To the right there's buttons to edit and reset the link. You want to reset. This forces Drupal to reevaluate the link.
It refreshes and poof! Gone from navigation, from add content page as well.