They claim it's because moderation tools are better on 3rd party apps, the truth is that they just don't want to see ads.
Pretty unanimously, 3rd party app developers have said they'd happily show Reddit's ads in their feed, but Reddit never came out with this feature. I don't think any 3rd party app developer was expecting a free ride on Reddit's API forever.
Pretty good read, you might have already read this: https://www.reddit.com/r/apolloapp/comments/144f6xm/apollo_w...
https://www.reddit.com/r/modhelp/comments/orqnr2/recommendat... https://www.reddit.com/r/modhelp/comments/t5t9n2/whats_the_b... https://www.reddit.com/r/apolloapp/comments/11w5ky3/a_review...
https://www.reddit.com/r/reddit/comments/145bram/addressing_...