You are absolutely correct.
Just backing up your iPad or iPhone to iTunes does not save any of your icloud files.
Any document saved to iCloud is NOT backed up anywhere in any of your backups in time machine or iTunes.
They are effectively "owned" by Apple (i.e., held hostage by iCloud).
They don't tell us this!
You think your work is safe. It's not. It's ONLY in the cloud. It's not even saved anywhere permanently on your own mobile device.
If the cloud becacking up your iPad or iPhone to iTunes does not save any of your icloud files.
I work for three months on dozens of Pages files from an iPad that was not connected to the Internet.
When I later set up a brand-new iMac with Lion the new iCloud sent a signal to my iPad on the very first time it was connected to the Net and all of my files were then instantly deleted right before my eyes. I thought everything was safe in my Time Capsule or in iTunes and my other drive backups of time machine and iTunes. But nothing had been saved anywhere because any iOS file tagged as owned by iCloud is NOT saved OR backed up. Apple was no help recovering them and took no resposibility.
Rely on the iCloud at your own peril. Just as any hard drive will eventually crash so will your iCloud files.
JC
Atlanta