I also had the same problem.
The French laws oblige me that the %VAT is visible.
I also lost a lot of time finding a solution.
Here’s what I did.
Go to plugins/woocommerce-pdf-invoices/includes/templates/invoices/simple/micro
Save body.php file
Edit the file at line 64 and replace
<? Php echo $ column_label; ?>
by
<? Php echo $ tax_label; ?>
You can now translate VAT using WPML and thus manually add % of VAT.
