Board Thread:Support Requests - Getting Technical/@comment-5065259-20131110232222/@comment-452-20140924150546

Do you have "Show hidden categories" enabled in your options?

(If not, please link to the category or page in question and I'll take a look)

If you also select "Disable Category module", the hidden categories are shown on a separate line.

You could also use .category.hidden to target the hidden category links with CSS to make them appear different.