[Ed B.]

• A very dirty but quick solution: find the twig file responsible for outputting the header, find the loop within, and add an if clause so that categories with certain category_id won't be shown. This is the quickest but will not survive to the update of the skin template module.
• A slightly cleaner solution: write your own module (maybe this is possible just playing with themetweeker, but I am not sure) so that the part of the twig file in the paragraph above gets overwritten...
• More time-consuming but probable far better solution, especially if you plan to add/delete categories and subcategories: write a module so that in the category editing page, you will have the choice of show and hide the category in the header menu. Go through the developer documentation https://devs.x-cart.com to find out how. There is a page explaining how to add properties to products, you can use the same method to add properties to categories, except that to deal with categories, x-cart doesn't use DTO as with the products.