I do the same thing. Apple is unclear about this, however. ApplicationSupport is at /Library/Application Support, and /Library definitely does get backed up to iTunes.
That said, I think we're in the clear with respect to iCloud backups:
"Devices with an active iCloud account have their app data backed up to iCloud at appropriate times. And for devices that are plugged into a computer, iTunes performs an incremental backup of the app’s data files."
It's ambiguous. But "app data" sounds like documents, whereas "app's data files" sounds like big data files in /Library to me.
http://developer.apple.com/library/ios/#DOCUMENTATION/FileMa...
That said, I think we're in the clear with respect to iCloud backups:
"Devices with an active iCloud account have their app data backed up to iCloud at appropriate times. And for devices that are plugged into a computer, iTunes performs an incremental backup of the app’s data files."
It's ambiguous. But "app data" sounds like documents, whereas "app's data files" sounds like big data files in /Library to me.