If you right-click on the Update button you get the option to hide the update. I assume this persists until you decide to unhide the update but I have never tried it.
If you are sure you will never use the original software again then delete it from your hard drive and updates will not be shown in future.
The app store counter is at "1" because it has an update for me to download and install. But this update is for stuff I don't have or use, therefore I don't want to install it. How to I get rid of it (decline it/reject it) ? Running Mountain Lion on a MacBook Pro.