Mac App Store Update issue in Yosemite
When I have had problems with the App Store, I have found that the boot volume was entered in the System Preferences -> Spotlight -> Privacy pane.  If the boot volume is included, it is EXCLUDED from the Spotlight indices, and the App Store uses those indices to determine what applications are installed.  

Once the volume is removed, and the indices updated (you have to wait...), the App Store started finding updates.