Hide empty product categories from menu

Hello everyone,
I have created the main menu from Appearance – Menu and I want to hide the empty product categories from it (only on frontend).

I have used a php snippet on functions.php but althought it hides the empty categories, it creates two problems.
1. The non empty category is displayed as top menu (besides Home, Shop, Contact etc instead of submenu to Shop)
2. Shop submenu is some other block/widget – I couldn’t find out – that contains the theme’s default megamenu items.

Here is the code:

add_filter( 'wp_get_nav_menu_items', 'nav_remove_empty_category_menu_item',10, 3 );
function nav_remove_empty_category_menu_item ( $items, $menu, $args ) {
	if ( ! is_admin() ) {
		global $wpdb;
		$nopost = $wpdb->get_col( "SELECT term_taxonomy_id FROM $wpdb->term_taxonomy WHERE count = 0" );
		foreach ( $items as $key => $item ) {
			if ( ( 'taxonomy' == $item->type ) && ( in_array( $item->object_id, $nopost ) ) ) {
				unset( $items[$key] );
			}
		}
	}
	return $items;
}

I’m also attaching two screenshots withthe wrong and right menu.

Thank you in advance.

Thank you in advance.