The iTunes backup is encrypted if you choose it to be. iTunes actually backs up your Health data only if you choose the encrypted option.

As to pros/cons -
Pros - It feels like a much more stable backup, and even the backup gets backed up if you use Time Machine on Mac or somesuch on Windows. I often run into iCloud storage issues (why doesn't Apple just make backups exempt from iCloud storage is beyond me) and have to delete my cloud backups of my iPad.

Cons - it takes forever! I hate backing up on iTunes because it's such a long time, is literally an all or none process, and I've not yet been able to figure out wireless backups, so I have to attach my cable every time I backup. This, of course, means fewer backups for my devices.

Con all around - Apple's backups are very opaque, specially on the cloud. I can't just backup some section of the device, like photos or settings, and I can't refresh specific sections of the backup either. This just adds to the lag time and causes us to live on the edge.