Remove submenu item from list

Use the API functions remove_menu_page and remove_submenu_page to remove menu items rather than manipulating global variables.

This will remove the themes page under appearance:

function wpa_remove_themes_submenu() {
    remove_submenu_page( 'themes.php', 'themes.php' );
}
add_action( 'admin_menu', 'wpa_remove_themes_submenu', 999 );