I have always suspected the poker sites themselves are running bots. But I have no proof.
While I could certainly go all "conspiracy theory" here, that's not what I'm trying to imply... basically, my idea is that if sites are running their own bots, it would be no different than a live brick-and-mortar casino using "prop players", which for those not aware, these are players who are paid an hourly wage by the casino to show up and play poker on a specific schedule. Prop players use their own bankroll, and they play their own game of poker. But the casino chooses to pay prop players for the reason that these props help to fill the tables up at slower times of the day (such as in the mornings)... and a full casino is a happy casino.
Poker players don't like to walk in and see an empty poker room, they want to see a full poker room with lots of action. Most players would never even realize if someone is a prop player or not, they are not identifiable and they don't have to tell other players they're a prop. There's nothing nefarious going on with prop players in a casino, and to wrap up my analogy, this is my own personal feeling that if an online poker site is running their own bots, they're used in the same way as props. Of course I realize a bot can play "perfect" poker (depending on how well the bot's programming is), but let's not get into the conspiracy theory angle. hahaha