Filter out products from search if they are hidden from catalogue as WooCommerce doesn't do this per default.

functions.php

<?php

add_action( 'pre_get_posts', 'set_posts_per_page' );
 	function set_posts_per_page( $query ) {

		if( !is_admin() ) {
			if( is_search() ) {
				$tax_query = (array) $query->get( 'tax_query' );
			    $tax_query[] = array(
			           'taxonomy' => 'product_visibility',
			           'field' => 'slug',
			           'terms' => array( 'exclude-from-search', 'exclude-from-catalog' ),
			           'operator' => 'NOT IN'
				);

			    $query->set( 'tax_query', $tax_query );
			 }
		}

 		return $query;
 	}

	add_action( 'woocommerce_product_query', 'yanco_woocommerce_custom_pre_get_posts_query' );
	function yanco_woocommerce_custom_pre_get_posts_query( $query ) {
		if( !is_admin() ) {
			if( is_search() ) {

			    $tax_query = (array) $query->get( 'tax_query' );
			    $tax_query[] = array(
			           'taxonomy' => 'product_visibilty',
			           'field' => 'slug',
			           'terms' => array( 'exclude-from-search', 'exclude-from-catalog' ),
			           'operator' => 'NOT IN'
			    );

			    $query->set( 'tax_query', $tax_query );
			}
		}

		return $query;

	}