I don't believe the OneNote Metro app supports indexing handwritten notes.
If you open the same notebook in the Win32 client and allow it to index and sync back to Sky/One/WhateverIt'sCalledThisWeekDrive you should be able to search through previously handwritten and Win32-client-OCRd notes in the Metro app.
If you open the same notebook in the Win32 client and allow it to index and sync back to Sky/One/WhateverIt'sCalledThisWeekDrive you should be able to search through previously handwritten and Win32-client-OCRd notes in the Metro app.