Well since from your signature it is apparent that you are familiar with 7+ Taskbar Tweaker. It has a Taskbar Inspector feature which lets you view the AppID of the running desktop app. For Modern apps installed from the Store, a quick way to see the AppID is the %LocalAppData%\Microsoft\Windows\Application Shortcuts folder. You can also see the AppID in the Registry as that MSDN article says.
The way to hide a shortcut that uses AppIDs is to create a subkey NoStartPageAppUserModelIDs at HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\FileAssociation and add the AppUserModelID there as string value. AppUserModelID can be found by going to key at HKCR\ActivatableClasses\Package\<packagename>\Server\<packagefullname> string value AppUserModelID.
Or you can type shell:::{4234d49b-0245-4df3-b780-3893943456e1} into the Run dialog/Start Menu's search box and enable the AppUserModellID column for the folder that opens, switch to details view to view the AppUserModelID.
Yes I know it's a rather annoying and painful process to block shortcuts by their AppID. NoStartPage is easier. If you can get TweakUI running on Windows 7, it lets you hide shortcuts by adding NoStartPage. The 32-bit version of TweakUI released by Microsoft works on Windows 7 32-bit in XP compatibility mode+set to Run as Administrator. For 64-bit Windows 7, you need to download the 64-bit version of TweakUI from
http://neosmart.net/TweakUI/ and also get Microsoft's Application Compatibility Toolkit 5.6, run the Compatibility Administrator tool as admin. Create a shim (Application Fix) for TweakUI with the Win2k3SP1VersionLie and Run as admin.
Maybe someone in the community can code an app to hide frequent programs that adds NoStartPage as well as the AppUserModelID for shortcuts that use it.