Why not simply charge for the API, and let Apollo figure out a funding model that works for them. It could be subscription, it could be going with a different ad server.
Having Reddit need to do audits of clients (where the clients could do things like quietly reduce the number of ads you get if you've tipped $9.99 or more - or not serve ads if your ID is on this special list so that friends don't see the ads or use a developer special trial build) is impractical and would mean that its even more of a call of if the client is in compliance or not.
What's more, ads served by the API to a client that isn't controlled by Reddit are less valuable - Reddit would have less information about how much engagement they had with the ad.