It seems to me that the simple way is pretty much what the grandparent described. Classify API/mobile access as a value-add and charge extra for it.

For a web-based SaaS, I could see them doing something like "Web-only access including mobile web, $10/mo" and "Web + native mobile/API access: $15/mo" -- then only offer the latter option in-app.

I suppose you could try to classify Android and iOS API access differently, but I suspect that might be a little over the line in terms of trying to slip it through the app store review process.

I do still wonder how third party apps to hit a subscription API are going to work, though. I suppose a lot of those will be for-pay so Apple gets their vig from that anyway, but it's always possible someone will decide to release a free one...