Third-party apps don't show ads; there's no reason ads couldn't be included in the feed and required to be shown as a condition of using the API, but I imagine it makes tracking impressions etc far more difficult. Any new features they add also need to either be incorporated into the API or remain unavailable for those users.
My only hope is that third-party apps remain niche enough that Reddit leaves them be; the first-party experiences are all awful to the point where I would probably just stop using Reddit if third-party offerings become unavailable.