Deleted the Content Type now cannot delete or edit node of that type, but it is visible on site
Ideally you should re-enable module which supports that custom node type, so the node can be properly removed.

Otherwise, you can load, edit or delete the node grammatically.

For example, to load the node using drush command-line, you can run:

drush ev "var_dump(node_load(1234));"


To delete it, try:

drush ev "node_delete(1234);"


Alternatively, you can delete these nodes from the node table.

To find all other references, check your database, e.g.

drush sql-dump --ordered-dump | grep my_node_name