Salesforce Enhanced Note is saved in both ContentNote and ContentDocument object with the same record id 069xxxxxxxxxxxx. By default, only the note owner or someone has been granted Viewer or Collaborator permission will have access to the Note.
When an Admin user query ContentNote object without specifying the record id, only the note has been explicitly shared with the user thru ContentDocumentlink will be returned. This behaviour has been documented here.
To allow a user to query all notes without having to specify the note record id. ‘Query All Files’ App Permission can be assigned to the user thru Profile/Permission Set.