Nick here from Shopify. Great question!
To remove an app subscription you would need to go to the App tab in your admin and then select the trash bin on the app you want to remove and you can remove it. It will look something along these lines:
Something to remember is charges might still show on the next invoice though, because the charge may have been generated for a billing period that started before the app was deleted. Shopify has a helpful guide going through everything you need to know about App charges which you might find useful here.
Hope this helps.
All the best, Nick