Yes, it is not something that you "set". Perhaps a better way to think about it is that you have X amount of apps that you have available to you in according to your plan level.
They allow some leeway so that while an app is initially under development with just a bit of test data and only 2 users (typically the App developer and maybe 1 user who is testing), then it does not count against your app limits. But once the app appears to have been deployed, then it counts.
You are right that while it is nice sometimes to be able to archive an app and hive off old data, that does count against your app limits.
