After a lot of issues, we have removed the 'Shop' app from our store, and the associated payment method. In short, it was more trouble than it was worth. Although it was quite convenient for people to use it to pay, it had the downside of repeatedly sending customers follow up emails with tracking info that didn't exist, and forcing them to sign up to their app.
We didn't like our customers being repeatedly told they need to download and register with an app that they really don't need, so we've removed it.
We still take most major credit & debit cards, and Paypal, so payments aren't really affected.