add_filter("woocommerce_product_query_tax_query", "hwn_hide_shop_categories");

function hwn_hide_shop_categories($tquery) {
    $hidden_categories = array("tshirts", "hoodies");
    if (is_shop()) {
        $tquery[] =
            array(
                "taxonomy" => "product_cat",
                "terms"    => $hidden_categories,
                "field"    => "slug",
                "operator" => "NOT IN"
        );
    }

    return $tquery;
}