If apps that were installed through the Windows store are not listed in Add/Remove Programs they will indeed not be scanned as installed software currently.
It may yet be possible to scan Windows Store app currently though, either through
custom registry or through
custom file scanning. Custom File scanning may be the best options as Windows Store apps appear to be installed in the following directory: Program Files\WindowsApps
This is an item on our customer wishlist though at this moment in time we don't have an estimated release date for this.