After some less than rigorous testing, I believe that if you mute a whole category then everything works as it should but if you only mute certain threads then the count in the tab still comes up to show there is something new to look at. 
This came up after the latest post in ‘Guess the person…’ which I have muted:
which makes it a little harder to keep an eye on forums because the system ‘cries wolf’ through no fault of the posters.