Can I reset Notification Centre badge counter for Messages?
The correct answer to this issue isn't to message all your contacts. 

First close the Messages app.

Then simply open up Activity Monitor and quit the Dock process to restart it.

Here's how it looks:



Your badge count should be reset after that.

PS: You can access Activity Monitor from Spotlight (⌘ Space) by simply typing its name and pressing Enter.

Edit: update thanks to @JjP and @Toland H