The box gets added in wp_nav_menu_setup(), so you’ll have to remove it sometime after that and before it’s being output later in nav-menus.php. There don’t seem to be any action hooks you can use there, but admin-header.php has a few. You could try this:
add_action( 'admin_head-nav-menus.php', 'roots_remove_nav_menu_metaboxes' );
I’ve never tried removing metaboxes from the menu screen, though, and it’s untested, so no idea if it works.