This depends on a number of factors that determine how VAT is calculated. First check the VAT options from the admin environment to make sure they are set correctly. To do this, go to the module settings, VAT tab.
1. Is VAT control on? This is essential as the system then behaves correctly to calculate VAT. The VAT check is done via VIES (VIES VAT check).
You can also set a deadline (interval) for checking the VAT numbers. An overview is then sent by e-mail that also shows all invalid VAT numbers. This concerns the option 'interval for VAT notifications'. VAT will therefore always be calculated for these customers.
2. Is the VAT calculated correctly but do you want to hide the VAT line? Then choose the option 'Show VAT on order confirmation' with preference >0.