I have the same problem (i.e. notification badge on my messaging icon falsely showing 1 unread message).
I have a totally stock Droid RAZR MAXX HD running 4.4.2. My stock messaging app is version 4.4.2-10. SMS is set to "Messaging" (not "Hangouts"). All settings are default. Verizon is my service provider.
I have tried all remedies suggested above, plus several of my own, all with no success.
From my own troubleshooting, I have concluded that the problem is probably KitKat-related since stopping, disabling, data clearing, cache clearing, and defaults clearing the stock messaging app all have no effect. Also, this problem started after upgrade to KitKat (never had it before). Further, after completely disabling the stock messaging app, I alternatively installed GO SMS Pro, chomp SMS, and Verizon Messages and experienced the same problem with each.
Any ideas about how to fix this problem, without having to FDR or root the phone would be greatly appreciated.