If my customer has autopay enabled, will the invoice indicate so?

Yes - if autopay is enabled on the customers profile

The invoice will indicate that the autopay will process automatically -

NO AUTOPAY:

If your customers Autopay fails 3 times in a row, Autopay will automatically be disabled for payment. Autopay can be enabled manually by the customer in the portal or from the customer's profile on the Hauler's view.

If your customer has an email on file for billing, they will be notified every time their autopay has failed.