Even after the Rules patch here https://drupal.org/node/1559844 I am still getting this token output as is in my order confirmation emails:[message:message-commerce-order:commerce-customer-shipping:commerce_customer_address].

This happens when a customer orders a non-shippable product and has not previously ordered a shippable product. For orders containing only non-shippable products, I have written a custom module to hide the shipping profile pane, and therefore the profile remains empty. I have tried hiding it both through "$checkout_pane['customer_profile_shipping']['enabled'] = FALSE;" and "unset($checkout_pane['customer_profile_shipping']);" but it doesn't make a difference for the token output.