On iOS 5.x the following code works as expected. Testing on iOS 6 beta 4 it appears that the callback is not called at all. This may also affect other callbacks in FileReader.
var reader = new FileReader();
reader.onloadend = function(evt)
Other research into this yields http://apache.markmail.org/thread/e4dhnq5qkn6ypprf which claims 5 of 95 tests in the File API fail on iOS 6 - though I have not verified this myself.