A Twitter user posted a video showing all the slashed Pokémon in his inventory, showing that the new measures are already live:

The "third-party services" in Niantic's post most likely pertains to a number of tools cheaters use, including spoofers that use fake GPS locations for those living in places where Pokémon rarely spawn. Some players also use mappers that tell them where powerful monsters appear, while others use bots to catch Pokémon for them.

It's unclear what the developer means by saying that the flagged monsters may not behave as expected. Will they just flop and die in the middle of a battle, or will they leave their owner's inventory altogether? According to Kotaku, some players are already reporting that the marked creatures don't give trainers candies when transferred to the Professor. They seem to lose their marks when evolved, though that's likely a bug or an oversight that Niantic may fix that in the future.