If you're VAT registered then you will need the add VAT to your invoices, even if the applicable VAT rate is zero which would make the VAT on the invoice due £nil.
If you can't see the VAT line on your invoice then please try the below:
Head over to the settings tab
Open up the VAT settings
Ensure that you have set your company as VAT registered and completed all fields
Click Save details
Do also ensure your HMRC business government gateway account is connected via Settings > Manage Connections.
If you still can't see VAT on your invoice after trying the above, please reach out to support.