I'm also having this issue, I'm stuck with a Shopify legacy app full of out of stock products with no way to delete. Even when I delete them manually product count sticks at 40.
The app ID doesn't correspond with any app ID in my business manager, so I'm stuck on what I need to delete to remove it.
Facebook have said the below, but you get a different answer from every agent so could be innaccurate, as the app ID for my Shopify app doesn't match the 'legacy app id':
"After having a look I can see that this App is the Shopify App itself so you will need to remove this within the Shopify interface on your Shopify account."