I have this same problem.
On my phone, when I go to Notes, and then click back to Accounts (top left) I see three entries:
All Notes
On my iPhone
iCloud
"On my iPhone" has all my notes that I've created over the years. iCloud has none, which is expected because I just enabled iCloud on my phone hoping my notes would get placed in iCloud.
These notes used to be accessible via Mail.app in OS X 10.7 (Lion). Now on OS X 10.8 (Mountain Lion), I cannot see these notes anymore in Mail.app. And they are not present in Notes.app or Reminders.app either.
I enabled iCloud on my iPhone to see if my notes would switch over, but they stay categorized as "On my iPhone" and don't move over to "iCloud." The iCloud syncing is working fine, I can create new notes in the iCloud account and I can then see them in my Mac. My concern are my already-existing notes. Years worth. Mailing them one by one is not feasible.
Since upgrading I have no way to access my "On my iPhone" notes from Mail any more. And it's not an option in the account preferences: http://imgur.com/z9N5H
So I was hoping to see my notes in the new Notes.app, but this is what it looks like on my screen: http://imgur.com/jX4u0
I see a categorization for iCloud and got Google (the latter is because I have Google notes enabled on my Mac, note: not on my phone). But I do not see a categorization for "On my Mac" (which is what I had in OS X 10.7 Lion wihin Mail.app).
I am considering for the first time jailbreaking my phone just so that I can extract these Notes from my iPhone through unofficial means (like copying the actual Notes database out of the iPhone via ssh). I hope to then restore my phone to factory and get rid of the jailbreak.
But I'm hoping someone with some smarts and a bright idea presents a solution. I am also working on finding one myself.