Hide default menu items in wordpress apearance > menus

You will able to remove nav menu meta-box links from screen option but if you want to remove by custom code, please try below code, simply copy and paste this into your functions.php file:

function custom_remove_menu_link_types() {
    global $wp_meta_boxes;
    foreach ($wp_meta_boxes['nav-menus']['side'] as $nav_menus) {
        foreach ($nav_menus as $nav_id => $nav_menu) {
            // remove all menu's and keep only one
            if ($nav_id !== 'add-custom-links') {
                remove_meta_box($nav_id, 'nav-menus', 'side');
            }
        }
    }
}
add_action('admin_head-nav-menus.php', 'custom_remove_menu_link_types', 10);