I've looked at a few questions (including this one) that answer related questions, but not the exact same. Is it possible to link to applications that don't yet exist in the iTunes store and also use affiliate links? I know it's possible to link to apps by using links like http://itunes.com/apps/amazon, but those don't use affiliate links. And I know I can generate affiliate links by going through linkshare to generate links, but that doesn't work on applications that aren't live yet.
Is there any way to do both?
Yes, you can affiliate encode essentially any iTunes link. There are two ways to do this.
Manually - Use the "Bulk" tool in the Link Maker (be sure to access the Link Maker from the affiliate network of your choice or it won't have been passed the appropriate affiliate tracking parameters).
Programmatically - Follow the instructions laid out here - http://www.apple.com/itunes/affiliates/resources/documentation/linking-to-the-itunes-music-store.html#AddingAffiliateTracking