It won't delete any app data, upgrading the OS does not touch the application's data at all. You can test this yourself, if you have iOS 6 installed, you can install the iOS 7 beta by Option clicking the "Check for Update" button, and select the ipsw. Whilst Apple don't suggest you do this, as it is still in beta, it's possible and demonstrates the upgrade path that users will take. I know OTA is slightly different, but the end result is the same.
Think about it, if wiping did occur, a lot of people would be extremely angry that their documents and game progress were lost due to an OS upgrade.