Hiding all posts/products/pages from a site based on a custom taxonomy/domain name

From the Codex for pre_get_posts:

pre_get_posts cannot be used to alter the query for Page requests (page templates) because ‘is_page’, ‘is_singular’, ‘pagename’ and other properties (depending if pretty permalinks are used) are already set by the parse_query() method. See: Query Overview. The recommended way to alter the main query for page requests is to use new WP_Query in the page template itself.

So, I’d suggest seeing if new WP_Query ( http://codex.wordpress.org/Class_Reference/WP_Query ) could help you here.