To add the customer's VAT Number to their invoices for legal purposes in the EU and some other countries, you can do so by going to: /components/invoice_templates/default_invoice/default_invoice_pdf.php
And adding the following line:
if(!empty($this->invoice->client->settings['tax_id']))
$address .= $this->invoice->client->settings['tax_id'] . "\n";
Please note this will be overwritten on update.