I've restored from an iCloud backup before, even data in third-party apps were restored. But any apps no longer avaible in the app store will not be restored as app binaries are not backed up by iCloud. But you can always backup locally to the Mac/PC once in a while for the peace of mind.
If you sync your apps with iTunes, you get the ability to rearrange apps and app pages in iTunes. You can also download app updates with iTunes first then sync to both your devices later.
Updating more than a few apps on iDevices can be slow and unreliable. A lot of times large apps (100MB-1GB+) get stuck downloading, and they'll keep the rest of your download queue from downloading and you can't even run those other apps because of the empty download bar and you basically have to reset. And even after you reset, the partial download of the large app with remain in the temp storage (it'll show up as "Other" in your storage usage map in iTunes). The only official way to clear those "Other" storage is do a restore. I myself have PhoneView, so I went into the iDevice and delete those files myself when a couple partially downloaded games took up over 2GB. There are people see it blow up to 5-6GB. Normal "Other" usage should be around 1GB.
Also, be careful when you turn of App sync, it'll ask you if you want to keep apps on your iDevices, click "Keep" or it may remove all your third-party apps and data on the iDevice and have to restore from a most recent backup.
That said, I use iCloud for backup and sync. As a general safety measure, I always perform a local backup in iTunes before I switch any iCloud sync options to/from iTunes.