Main reason bots still disabled?

The only reason bots went down was that Niantic changed their API and the reason they're still down is that the API hasn't been hacked yet. The exact same thing has happened before, although the API got hacked faster after the change.

We can guess on Niantic's reasons for this, but it's a bit hard to look at it as a conscious effort to put out bots because they didn't need this to disable bots, they have always had the ability to identify and ban them from the first login.

You have a very good point. But it is likely not about them not charging as much as the sponsors not paying. I am also guessing there is a specific set of hours that sponsors will pay for stops and some math being done where some are calling BS. This is all good and will work itself out.