If you look at my links to the costume sites above, you'll notice the top level categories do not show on the respective sites, only those second level categories under the site category.

Breadcrumbs have also been customized to remove the unecessary category links.

Sideboxes and special lists (featured, special etc.) were all mod'd to only show the correct sites (via top level category) items.

Its all possible, just takes more time to get the finer details.