Snippet to hide specified shipping methods with zero cost. PluginHive Plugins : https://www.pluginhive.com/plugins/

functions.php

/**
 * Snippet to hide specified shipping methods with zero cost.
 * Created at : 07 Nov 2018
 * Updated at : 07 Nov 2018
 * PluginHive Plugins : https://www.pluginhive.com/plugins/
 * Gist Link : https://gist.github.com/varun-pluginhive/a7b88d265b5ecb89d823ffe9d06daf7c
 */
add_filter( 'woocommerce_package_rates', function( $shipping_rates ){
	$shipping_methods = array( 'wf_woocommerce_shipping_pro:1shipping-pro-1');		// Array of Shipping method ids

	foreach( $shipping_rates as $key => $shipping_rate ){
		if( in_array( $shipping_rate->get_id(), $shipping_methods ) ) {
			$shipping_cost = (double) $shipping_rate->get_cost();
			if( empty($shipping_cost) )
				unset($shipping_rates[$key]);
		}
	}
	return $shipping_rates;
} );