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:
Enabled
Disabled
Enable if
Disable if

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.