When you edit a article, category or comment you'll see an option toward the bottom to hide it. If it's set to no, then it's not hidden and will appear normally. If set to yes, the item will no longer be listed anywhere but will still be accessible to anyone who has a link to it. This can be useful for retaining search engine traffic to outdated info (by default, expired articles are hidden), or to have a special category or article linked in a different way/place than the rest.

Note the distinction between a hidden item and a soft-deleted item. A soft-deleted item is not accessible even if you know its URL.

Since hidden articles/categories aren't displayed in categories or search results, you'll have to go to a special place to find a list of them to edit. Go to Admin Panel -> Common Tasks -> Search and see the "Hidden Items" options at the very top.