I am still seeing this in the subject in the emails received. Also, we needed the shortcode in order for this to show a product code in the subject line so we could filter emails on the server. Ultimately, your product does not have what j2store and virtuemart has, which is more flexibilty on how it sends emails.
We currently have different locations which take the order, so when someone orders a product, that product shows up with a code we added to the subject line per location. When that code shows up in the subject, it automatically is detected on the server and an email gets sent to a specific location. This was the only way to do this due to lack of flexibility with easystore. I love the product, don't get me wrong, but this was the only way I could overcome this issue. Unless there is a way to add another shortcode that specifically pulls that product code so my server can filter the email.