I don't think they are missing, most probably they're inside a fence and that fence was accidentally moved to another desktop page.You can try few things:
1) Switch the desktop pages, "alt"+ "Left or Right arrow" on the keyboard.
2) Reset Fences to it first use state by Layout snapshot as suggested by Azdude above, just instead of restoring yesterday snapshot, try restore the "First Use Snapshot" that should bring back all the icons. Make sure you saved your current setting before you do the restore.
Try that and let us know.
Stardock Community Assistant