I believe that many users of Pipedrive may close a deal with an organization and that may be the only deal you close until the contract comes up again.  Additionally, I am not quite sure of a deal that could be in play with an organization that wouldn't be assisted by previous deal's notes or organization notes.

All that said I feel that the Organization Notes should be visible at the deal level.  If you want to make it a bit more dynamic have a filter at the deal level that switched between All notes / deal notes.