There may be a number of reasons why you may want to hide a category from the store front, this is easily done through the admin.

Products > Categories 

Select the status of the category...

Active - The pages are live and on the menus and site structure

Disabled - This denies ant access the the category page

Hidden - The pages are live but do not show up to users on the store front

All these settings still allow store admin to work with the category page and add products still.