I don't think anyone really knows at this point (it's debatable if the measure will even work), however, I suspect the real target of the blacklist apps are the ones that facilitate spoofing (GPS hacks etc.), or those that directly interact with the game data.
"Safe" tools like the overlay IV Calculators I personally don't think will be affected but, even if they are targeted, I suspect that the worse comeuppance you'll get is a warning, although repeated infractions may be a different story. Previous anti-cheating methods have generally given the players the opportunity to change their ways, e.g. rendered pokemon un-usable without immediately banning their accounts.