Craft Commerce Currency - Email template not showing currency
You need to pass the currency to the conversion filter.

The order is always made in the primary currency, but the payment currency that they made the payment in might be different, so you need to pass order.paymentCurrency to the conversion filter.

You can read about using different currencies here: 
https://craftcommerce.com/docs/payment-currencies

In addition to just changing the filter to |commerceCurrency take a look at the docs for the filter for the optional formatting and conversion options:
https://craftcommerce.com/docs/twig-filters