Emails from WP do not run shortcodes by default, you need to make that happen. There are some plugins that will do this or you can add code to your site.
add_filter('wp_mail', 'shortcodes_in_wp_mail', 20, 1);
function shortcodes_in_wp_mail($args) {
$args['message'] = do_shortcode($args['message']);
return $args;
}