Pokémon GO updates will have new deterrents for cheaters, and these seem to use shame more than just prevention. The changes were mentioned by a Pokémon GO support account on Reddit. (There are other updates coming soon to Pokémon GO as well.)
If the Pokémon GO app detects the use of third-party software, it will apparently now place a red slash over any Pokémon trainers catch while using that software. The red slash signals that they are a cheater even to other players, could possibly be visually disruptive to the affected players, and also goes along with changing that Pokémon's behavior.
Not only will a red slash appear over any Pokémon caught cheating, but those Pokémon will also misbehave for cheating players. It is unknown how the Pokémon's behavior will differ from usual; so it could be entertaining to see if you're not super competitive. Most cheaters, though, may not be that casual about it.
There are other updates coming soon to Pokémon GO as well.
Niantic has not specified which software will result in the marks — possibly to make it harder to find a way around the update. The minor war over cheating in Pokémon GO is controversial; some say the cheating is necessary to even the playing field, for those with impaired mobility, or who live in rural areas with fewer Pokémon.
Niantic seems sure, however, that it's the 3rd party apps creating the most unfairness. So if you choose to take a 3rd-party shortcut, keep in mind that your Pokémon — your closest allies in-game — will remember what you did, and they may not forgive you for it.