Very interesting article. I don't think anyone has doubted that bots existed, the real questions were whether it was widespread and whether someone could create a bot that was more than just a break even limit bot.
People should also be aware that in the genesis of online poker there was a ton of cheating and pot possibilities, but since then the online poker sites have beefed up their security to detect bots. With that being said i would be shocked if any major site is 100 percent bot free.
As far as winning poker bots, i have not seen much evidence that there has been a winning poker bot. Most were created, as was pointed out by the author, to simply break even at the tables, and then they get paid a ton in rakeback. Thats why WPEX was thought to be infiltrated with bots since they went rakefree.