Something tells me practically no apps will be seriously affected.
So they have to deal with arbitrary filenames; on the other hand, for the same reason, they can't maintain a master list of files somewhere which would break, but have to check the actual directory contents instead. Still, things like history or links between files might be broken.
That is, unless NSFileCoordination APIs act differently wrt normalization; iCloud clients have to use those rather than accessing the filesystem directly.
They should be doing that anyway. Anything else is just begging to get out of sync at some point.
Using a network value or a value returned by an API is just asking for trouble.
If a user names a file that will be hidden behind a URL the same advice applies. If not then the user can use any sequence of bytes they want and you shouldn't care.
It also means that, yet again, every app will need to be updated for a new version of iOS. Makes me wonder how many apps will be left behind if not updated? Thousands? Hundreds of thousands? Millions?