The way I did it, was add a column in the Category table called 'Visible' as an ENUM('Yes','No') type, defaulting to Yes then added the following at the top of the subcategory.html template:

Then at the bottom put:

Then you just put No in the categories you don't want displayed.

It simply doesn't add a link to the category on any page that uses subcategory.html to generate a list of them. This modification still allows you to see the category once the site is built, if you know it's name, so it is not for everybody, but it works for our purposes.

Hope that helps,
-Steven