Hm, is it possible that you have “Optimize Mac Storage” enabled? You can find that option in “System Preferences -> iCloud -> iCloud Drive”. I’d recommend to disable it because the data has to be fully available in order to decrypt them. If it’s already disabled, could you please look inside the log file if there are any errors?
I must admit that it doesn’t really explain why the directories are also missing on iOS. Maybe the files just haven’t been fully uploaded yet from your initial device?