Exclude specific products from a woocommerce list using a custom walker.

WooExclude_Walker_Category

class WooExclude_Walker_Category extends Walker_Category
{
  /**
	 * Start the element output.
	 *
	 * @see Walker::start_el()
	 *
	 * @since 2.1.0
	 *
	 * @param string $output   Passed by reference. Used to append additional content.
	 * @param object $category Category data object.
	 * @param int    $depth    Depth of category in reference to parents. Default 0.
	 * @param array  $args     An array of arguments. @see wp_list_categories()
	 * @param int    $id       ID of the current category.
	 */
	public function start_el( &$output, $category, $depth = 0, $args = array(), $id = 0 ) {
		/** This filter is documented in wp-includes/category-template.php */
		$cat_name = apply_filters(
			'list_cats',
			esc_attr( $category->name ),
			$category
		);

		$link = '<a href="' . esc_url( get_term_link( $category ) ) . '" ';
		if ( $args['use_desc_for_title'] && ! empty( $category->description ) ) {
			/**
			 * Filter the category description for display.
			 *
			 * @since 1.2.0
			 *
			 * @param string $description Category description.
			 * @param object $category    Category object.
			 */
			$link .= 'title="' . esc_attr( strip_tags( apply_filters( 'category_description', $category->description, $category ) ) ) . '"';
		}

		$link .= '>';
		$link .= $cat_name . '</a>';

		if ( ! empty( $args['feed_image'] ) || ! empty( $args['feed'] ) ) {
			$link .= ' ';

			if ( empty( $args['feed_image'] ) ) {
				$link .= '(';
			}

			$link .= '<a href="' . esc_url( get_term_feed_link( $category->term_id, $category->taxonomy, $args['feed_type'] ) ) . '"';

			if ( empty( $args['feed'] ) ) {
				$alt = ' alt="' . sprintf(__( 'Feed for all posts filed under %s' ), $cat_name ) . '"';
			} else {
				$alt = ' alt="' . $args['feed'] . '"';
				$name = $args['feed'];
				$link .= empty( $args['title'] ) ? '' : $args['title'];
			}

			$link .= '>';

			if ( empty( $args['feed_image'] ) ) {
				$link .= $name;
			} else {
				$link .= "<img src='" . $args['feed_image'] . "'$alt" . ' />';
			}
			$link .= '</a>';

			if ( empty( $args['feed_image'] ) ) {
				$link .= ')';
			}
		}

		if ( ! empty( $args['show_count'] )) {
                        $pargs = array(
                            'post_type' => 'product',
                            'post_status' => 'publish',
                            'tax_query' => array(
                                array(
                                        'taxonomy' => $category->taxonomy,
                                        'field' => 'term_id',
                                        'terms' => $category->term_id
                                )                                
                            ),
                            'meta_query' => array(
                                array(
                                    'key' => 'special',
                                    'compare' => 'NOT EXISTS'
                                )
                            )
                        );
                        $pplist = new WP_Query($pargs);
                        wp_reset_postdata();
			// Original count
                        // $link .= ' (' . number_format_i18n( $category->count ) . ') - ';
                        $link.=' ('.number_format_i18n($pplist->found_posts).')';
		}
		if ( 'list' == $args['style'] ) {
			$output .= "\t<li";
			$class = 'cat-item cat-item-' . $category->term_id;
			if ( ! empty( $args['current_category'] ) ) {
				$_current_category = get_term( $args['current_category'], $category->taxonomy );
				if ( $category->term_id == $args['current_category'] ) {
					$class .=  ' current-cat';
				} elseif ( $category->term_id == $_current_category->parent ) {
					$class .=  ' current-cat-parent';
				}
			}
			$output .=  ' class="' . $class . '"';
			$output .= ">$link\n";
		} else {
			$output .= "\t$link<br />\n";
		}
	}
}

add_filter('woocommerce_product_categories_widget_args','test_filter');
function test_filter($list_args) {
    $list_args['walker'] = new WooExclude_Walker_Category();
    return $list_args;
}