All email templates can be enabled / disabled. It would cover a whole range of user cases when you would add a feature that would allows you to conditionally enable an email template based on system variables.
My user case. I have a direct debit payment method. Users that have chosen this payment method are annoyed by the extra payment reminder. I want the cash payers to receive a reminder, not the Paypal subscription and Direct debit payers.
4 Radio buttons and a textarea would do. The radios choices:
The last two choices would activate the textarea where you can list the system variable tests (one per line) to evaluate. In the given user case I would click the radio "Disable if" and put conditions in the textarea that test the presence of Paypal subscription and the direct debit payment type.