It still shouldn't be doing that. I have about 1200 notes (including lots of graphics), and even turning off my iCloud Notes and turning it back on it takes about 5 minutes to sync, and I do get the 20-130% CPU usage, but the vast majority of that time it's on the low 30%-end for me.
Now my Notes would show the syncing/busy icon on the app window itself, is that what you mean? Or do you mean your mouse cursor is literally changing to a busy mouse/beach ball? Mine does not beach ball even for a second, so I think there is a hard drive/file system/file issue going on with yours.
Here is what I would do:
- Quit Notes, turn off iCloud Notes again.
- Copy the files in your Notes data storage folder (~/Library/Containers/com.apple.Notes/Data/Library/Notes/) and paste that copy somewhere (like on your Desktop)...just in case.
- Remove the contents of that Notes data store folder into the Trash, and empty your Trash.
- Run a First Aid/Disk Scan for good measure
- Finally, enable your iCloud Notes again and let things sync.
If you still get beach balls at all, or if this takes over 30 minutes there's definitely something else going on, but hopefully that won't be the case and this will in fact clear things up for you.