The folder Notenik creates on the iCloud Drive can not be found by the macOS search.
Not sure why this would be the case. You can always store your Notenik collections somewhere else if you would like. Notenik is a sandboxed app, so it generally doesn’t ask for any extraordinary permissions, but then by default it stores your collections (aka folders) in the Notenik folder within iCloud drive, which it should always have access to.
This seems to be a similar issue reported more generally by someone else: Finder search not showing iCloud documents - Apple Community
But also, perhaps, be careful to select iCloud Drive as your search location, rather than your Macintosh HD (or some other location).
Hope some of this helps. And welcome to the Notenik discussion forum!