The other cynical person would say that doesn't make sense because out of the very small amount of people that backup via iTunes, an extremely small percent of them would actually bother encrypting.
If you don't encrypt the backup, then iTunes does not backup your stored passwords (wifi WPA2, web, mail, etc), health data, and other items considered "sensitive", which makes for a poor backup/restore experience. So there's a big benefit in enabling encryption in iTunes.
It's a bit annoying considering macOS can also use FileVault for full-disk encryption, which helps if the machine is locked/off. I guess it doesn't help against your macOS user account being compromised via a browser or anything.
Makes me wonder if anyone has taken a fresh new look at the FDE passphrase algorithms in macOS 10.12...
