Limit the amount of meta boxes to pages, posts, links, and categories for first time users.

function wp_initial_nav_menu_meta_boxes() {
	global $wp_meta_boxes;

	if ( get_user_option( 'metaboxhidden_nav-menus' ) !== false || ! is_array( $wp_meta_boxes ) ) {
		return;
	}

	$initial_meta_boxes = array( 'add-post-type-page', 'add-post-type-post', 'add-custom-links', 'add-category' );
	$hidden_meta_boxes  = array();

	foreach ( array_keys( $wp_meta_boxes['nav-menus'] ) as $context ) {
		foreach ( array_keys( $wp_meta_boxes['nav-menus'][ $context ] ) as $priority ) {
			foreach ( $wp_meta_boxes['nav-menus'][ $context ][ $priority ] as $box ) {
				if ( in_array( $box['id'], $initial_meta_boxes, true ) ) {
					unset( $box['id'] );
				} else {
					$hidden_meta_boxes[] = $box['id'];
				}
			}
		}
	}

	$user = wp_get_current_user();
	update_user_meta( $user->ID, 'metaboxhidden_nav-menus', $hidden_meta_boxes );
}