I would strongly recommend you boot up under an external disk and run Disk Utility to fix both the permissions and the drive. Often when I see this when nothing has been altered the HD's Btree tables need repair. The other option here is to locate the files and just make new shortcuts. If you can't fix the pathing, you'll need to use the Select New Original button to relocate the file. If you see the error you may find fixing the Folder or Volume path easier than fixing all of the discrete shortcuts.

Right click the icon and then select Get Info Within the general section note the Original entry see if you can figure out what changed. To fix this you will need to open each shortcut and relink the original file. This could be caused by moving or renaming the folder or the volume the original file was located. It appears your shortcuts have lost there linkage back to the original files which is why you are seeing the generic icon vs the discrete icon the app or document would normally have.

Mac dock icons not showing