Hi,
I got some feedback from Kadence: "It's intentional that we show custom fields; removing the field in Meta Box doesn't remove the data from your posts, and since you can use many things other than Meta Box (like your own custom code) to create custom fields, we intentionally show all the fields that WordPress shows when we do a query, not just the fields that you've created with Meta Box. This means that if you make a field and add content, then that data is registered with WordPress, and you would need to remove it there (not just the plugin) for it to not show in our options."
I did remove most, if not all, field data from the posts before removing the fields themselves. WordPress is not very good in cleaning things up I guess, and after a while it's inevitable to delete old stuff from the database using plugins like you suggested.