The emails that are passed to UserNotifications#notification_email should be being displayed as rtl for rtl users. These are the emails that are sent for things like user_posted, and user_quoted etc. The other notification emails, the ones for things like signup and forgot_password and also the digest, are not being displayed rtl for rtl languages.
The fix for the digest is simple. I can make a pull request for that. The fix for the other emails (signup, forgot_password…) is a little more complicated because they are derived from templates, but the template isn’t wrapped in anything that you can give a direction to.