Can iOS apps be safely deleted from iTunes?
The apps can be safely deleted from iTunes without affecting either the apps currently on the device or your backups. When you perform a backup, all of your data is backed up regardless of the apps you have in iTunes.

However, when you restore from a backup, apps are re-download from the iTunes Store. If one of your apps is no longer available on the store for some reason, that particular app won't be restored. If you still have a copy of the app on your computer, you'll be able to install it on your device from iTunes. (I'm not sure what happens to the app's data in this case, however. I suspect it depends on whether you're restoring from an iCloud backup or a local backup, but I've never had the chance to test it.)