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The functionality to hide hidden fields in the Email is ON at all times.
The only time it will become OFF is if you modify or customize the email template (the Notifier or Autoresponder). So it will only work if you do not alter the email template (Notifier or Autoresponder).
You can test it by adding another Autoresponder E-mail on your form and leave everything as is. Do not alter the message body. You do can change the Recipient and Sender part..
Test submit your form to check if hidden fields in the form will not show in the email message.
Let us know if you need further assistance.