Can iOS apps be safely deleted from iTunes?

On my PC, the iOS apps synchronized by iTunes take up a pretty substantial percentage of my total disk space.

Since most, if not all of them, can be recovered from the App Store, is it safe to delete them on my PC?

I've already verified that removing apps does not affect any apps currently installed on my device; now I'm wondering if it might cause problems once I have to restore from a backup.

It seems as if the backup itself only contains the data of the applications, and not the apps themselves. What happens when restoring a device with most or all .ipa files missing in the iTunes folder; will the missing apps be downloaded from the app store, or will restoring the apps and their data fail?

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.)

When restoring your phone from a backup the applications, music, address book etc all get uploaded. If you do lose your apps they are always saved to your Apple Account so you can just re-download them, however sometimes you may lose the data saved within them i.e. a place in a game where you left of before.