OK firstly calm down Wiggum15....
...you're getting yourself rather worked up over a small feature of the phone. And I'm interpreting your tone on this thread as quite aggressive towards others. by all means explain there is an issue and talk it out with others but maybe reel it in a little eh?
After some looking around on-line i have found out that the issue IS an API restriction that Microsoft have added in. It ISN'T an OS restriction however.
An API (Application Programming Interface) is just that an interface. It's a layer between the OS and the App that allows the two to interact without being directly tied to each other. This as I am sure you can understand isolates and protects the two systems from each other in the event of failure or a malicious attack etc.
The reason the issue does NOT occur with features like the phone and messaging and eMail (outlook, Exchange etc) is because they are built into the core OS they don't need to use the API ( the have direct interaction instead) and have more freedoms available to them in how they function and update/interact with other OS functions.
Everything else however DOES use the API and therefore is unable to update the tile number when the notification is cleared from the action centre. I have observed this behaviour with Whatsapp (as previosuly mentioned by others) but also on Skype, Facebook Messenger, Facebook, 6tin, 6snap and Twitter (Those are the few on my start screen that have tile counts)
Until microsoft either change or update the API to allow this to occur i'm afraid you're stuck with it. The only thing i can suggest is that the issue is raised on the
uservoice page for windows phone . Again searching there i can see at least 3 other suggestions highlighting your issue. links here
Link 1
Link 2
Link 3
In future instead of attacking this community and insulting them (again my feelings based on what has already been said) try and contribute positively. Look on the UserVoice see if the issue has been bought up if so vote on it if not create your own. Then come here and raise a topic about it explaining the issue and asking people here who share your views to up vote that issue on the UserVoice. You'll find MS more likely to take note and then the feature could come along a lot quicker.