From what I can see Notes are now stored in a hidden folder. Even when you find them in Time Machine they are not recoverable. Send Apple feedback http://www.apple.com/feedback/ . This bug should be fixed as soon as possible.
Read https://discussions.apple.com/message/19171700#19171700 for info on where they are now stored. To open your Library folder open a Finder window then click the Go menu pressing the Option key on the keyboard to make Library appear.
Notes should be recoverable by entering Time Machine with the Note app open as other apps work. When I open the folder mentioned in the thread then open Time Machine all deleted and modified Notes get marked as "(Null)" and contain no data.
Thanks, I was able to restore and sent following feedback to Apple:
I was syncing notes with iMac and iCloud. I stopped sync with iMac, dialog box says notes will be deleted from iMac but remain on iCloud for use by other devices. That is not true. Notes were deleted from iMac, iCloud and thus the iPhone and iPad.