Only the apps that actively check for root. Mostly banking apps, some games (PoGo, PUBG, etc), Uber, McDonalds, etc.
Don't go on an adding spree. If you launch an app and see a warning, only then try to hide it.
Is there a way to include the fix while still letting users to "fix" it themselves in case Google breaks it again? I think it works on EvoX and Derpfest that way.