I just had the scare of the year with my Notes app also. I have been adding to one or two pages in the Notes app on my iPad Mini for over a year, and today when I went to look something up on one of them, ALL my notes were gone!! It was as if I was using the app for the very first time!! I nearly fainted!!
Mid panic attack, I brailled around Google and found this link. I didn't really know what to make of it other than that somehow there might be hope--my Notes might actually still exist SOMEWHERE:
http://gmail-miscellany.blogspot.co.uk/2013/08/gmail-apple-notes-app.html
After reading that, I went into Settings in the Mini. I didn't think my Notes had ever been asscociated with Gmail BUT I had occasionally emailed a Note via my AOL account on the Mini, so I looked in "Mail, Contacts, Calendars" and under AOL I saw that Notes had been togggled off. It must not have been like that before or I prpbably wouldn't have been able to email out a Note as I had done preveiously, so I toggled it on.
Lo and behold--ALL MY NOTES REAPPEARED in Notes!! Whew!!!
I notice that Settings>Notes>Default Account now says AOL, not My iPad like it did when my Notes were missing, so I assume AOL was how it was set originally.