You’ll find that ShellExperienceHost.exe and SearchUI.exe services are not running in the background, that’s why all modern UI elements such as Start Menu and Taskbar fly-outs don’t work. You can check it yourself by opening Task Manager. I think removing all apps triggers some check in the system which forces some system apps such as ShellExperienceHost.exe, SearchUI.exe, etc to stop working which are responsible to provide functionality to Start Menu and other modern (metro) UI elements as mentioned in “Important Note 3” given at the end of this tutorial. If you remove a few apps, it doesn’t cause this issue but if you remove all apps at once, it breaks Start Menu and Taskbar notification bar icons. It seems the problem is related to removing all modern (UWP) apps using PowerShell method in Windows 10 newer versions.

Users are unable to access Start Menu and Taskbar icons. Most of the times this issue occurs after installing new updates via Windows Update or after upgrading to a new Windows 10 version. When you sign in again, the problem still persists and the error message again appears when you click on Start button. When you click on “Sign out now” button, it logs off and shows login screen. We’ll try to fix it the next time you sign in.

Windows 7 user icons