I just started having this same problem. Don't use Notes much, but today for the second time in a week the notes disappeared when I launched the app on my ipad mini. Using Lion and iOS 6.1.2, so it's not a Mountain Lion issue for me.
I haven't been using iCloud.
Went into Settings --> iCloud and turned on Notes. Had to go back into Notes and select a Default account (set it to my yahoo email, as it preselected iCloud but again I'm not using iCloud). Lo and behold now I have a Notes file in my Yahoo email, and it contains the notes I lost today along with the note I had lost last week. This new Yahoo Notes file is not appearing on the device (ipad mini) which lost them in the first place, but I do see it on my iPhone and MacBook.
But wanting it on the ipad, I just emailed the note from my Yahoo acct to myself, and then was able to copy the info from Mail/Yahoo on my ipad into Notes.
I also went ahead and downloaded a different notes app just in case Notes screws up again, cuz I must say I have lost some faith in that particular app at this point.