Usually when you perform the upgrade from Windows 10 to 11, at the start of the process, if there is any applications installed that would be incompatible with Windows 11, there would be a notification that the upgrade would remove the listed applications, otherwise, the upgrade should not remove any of your applications.
How long has it been since you performed the upgrade to Windows 11, is it less than 10 days, and if the shortcuts have disappeared on your Desktop, if you perform a search for a missing application on the Taskbar search box, does that no longer find the application?