Remove nav_menus from customizer using a theme

Question

This is panel not section so remove_section() will not work in this case. However you can use function remove_panel() but it will trigger a notice saying

Notice: WP_Customize_Manager::remove_panel was called
incorrectly Removing nav_menus manually will cause
PHP warnings. Use the customize_loaded_components filter instead. Please see Debugging in
WordPress for more information. (This message was added in version
4.5.) in \wp-includes\functions.php on line 3897

Now customize_loaded_components filter says

This allows Core components to be excluded from being instantiated by
filtering them out of the array. Note that this filter generally runs
during the ‘plugins_loaded’ action, so it cannot be added in a theme.

So there is no straight way for removing menu section from customizer and using theme but if you like then I found a solution (May be not so good) which works without any warnings and errors.

In class WP_Customize_Nav_Menus constructor check for

if ( ! current_user_can( 'edit_theme_options' ) ) {
    return;
}

And then register all the action/filters for nave menu section thus removing all those filter/action can do the trick. But for removing those filters/action we need the same object which was used to register them. And yes we have it in customize_register action callback.

You can add this code to your theme functions.php

add_action('customize_register', function ( $WP_Customize_Manager ){
    //check if WP_Customize_Nav_Menus object exist
    if (isset($WP_Customize_Manager->nav_menus) && is_object($WP_Customize_Manager->nav_menus)) {

        //Remove all the filters/actions resiterd in WP_Customize_Nav_Menus __construct
        remove_filter( 'customize_refresh_nonces', array( $WP_Customize_Manager->nav_menus, 'filter_nonces' ) );
        remove_action( 'wp_ajax_load-available-menu-items-customizer', array( $WP_Customize_Manager->nav_menus, 'ajax_load_available_items' ) );
        remove_action( 'wp_ajax_search-available-menu-items-customizer', array( $WP_Customize_Manager->nav_menus, 'ajax_search_available_items' ) );
        remove_action( 'customize_controls_enqueue_scripts', array( $WP_Customize_Manager->nav_menus, 'enqueue_scripts' ) );
        remove_action( 'customize_register', array( $WP_Customize_Manager->nav_menus, 'customize_register' ), 11 );
        remove_filter( 'customize_dynamic_setting_args', array( $WP_Customize_Manager->nav_menus, 'filter_dynamic_setting_args' ), 10, 2 );
        remove_filter( 'customize_dynamic_setting_class', array( $WP_Customize_Manager->nav_menus, 'filter_dynamic_setting_class' ), 10, 3 );
        remove_action( 'customize_controls_print_footer_scripts', array( $WP_Customize_Manager->nav_menus, 'print_templates' ) );
        remove_action( 'customize_controls_print_footer_scripts', array( $WP_Customize_Manager->nav_menus, 'available_items_template' ) );
        remove_action( 'customize_preview_init', array( $WP_Customize_Manager->nav_menus, 'customize_preview_init' ) );
        remove_filter( 'customize_dynamic_partial_args', array( $WP_Customize_Manager->nav_menus, 'customize_dynamic_partial_args' ), 10, 2 );

    }
}, -1); //Give it a lowest priority so we can remove it on right time

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