It works for me on Zen Cart v. 1.3.7... Are you sure you got all the code?
That's because it isn't there ;-) I think the file that sends that email is /includes/classes/order.php or maybe admin/order.php. The corresponding language files are includes/languages/english/checkout_process.php and admin/includes/languages/english/orders.php. You could get the VAT-number from any of these files... We can do it for you if you make it worth our while :-)
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