PHone and Messaging icons do not show unread message notification or missed call in 4.04
I got the same problem a week ago and I found the solution myself by using "trial and error method" for my Samsung S3 mobile (Android 4.3).


Go to Settings > Application manager. There you will see turned off application which is named as BadgeProvider (in Android 4.3 it is in "turned off" application list but some version hasn't that "turned off" application list and in that situation you will see that application in bottom part of "ALL" application list.
So after you got that application you have to tap it and turn it on. 


Now your problem should be solved. (Sometimes you have to restart your mobile after this process).