This is a known issue with the fix required of removing your main hard drive from indexing through the Privacy screen. You may have to add the main hard drive to privacy first, then remove it, then restart, and allow the hard drive to be indexed again.
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.
For better technical details, see: Mac App Store: "Cannot update App Store purchases or updates do not seem available" and "Mac App Store Update issue in Yosemite"