Well, not every site deals with mobile traffic exclusively with an app. Even if you offer an app, you don't necessarily have to force mobile users to a page about it. In fact, while I know you're bringing this up in the context of affiliate links, as far as organic search is concerned, Google has been very clear in warning site operators that redirecting all mobile users to a single page (such as a page about your app) is a bad user experience.
But getting back to your original question, if your affiliates are paid for driving traffic to your site, then the traffic they drive to your app page should count IMO. If your program involves a revenue share, then revenue generated from your app ought to be part of that.