In that theme's header.php change:
echo preg_replace('@\<li([^>]*)>\<a([^>]*)>(.*?)\<\/a>@i', '<li$1><a class="fadeThis"$2><span class="title">$3</span><span class="pointer"></span></a>', wp_list_pages('echo=0&orderby=name&title_li=&exclude='.get_mystique_option('exclude_pages')));
to
if (is_user_logged_in()){
echo preg_replace('@\<li([^>]*)>\<a([^>]*)>(.*?)\<\/a>@i', '<li$1><a class="fadeThis"$2><span class="title">$3</span><span class="pointer"></span></a>', wp_list_pages('echo=0&orderby=name&title_li=&exclude='.get_mystique_option('exclude_pages')));
}
else {
echo preg_replace('@\<li([^>]*)>\<a([^>]*)>(.*?)\<\/a>@i', '<li$1><a class="fadeThis"$2><span class="title">$3</span><span class="pointer"></span></a>', wp_list_pages('echo=0&orderby=name&title_li=&exclude=2,'.get_mystique_option('exclude_pages')));
};
endif;
The key is this exclude=2,43,67, where the 2,43,67, are the IDs of the pages being hidden from users that are NOT logged in. Note those ID's are appended in front of the exclude ability that theme offers.
And just in case:
How do I determine a Post, Page, Category, Tag, Link, Link Category, or User ID?