After I upgraded to Win 8.1 64-bit Pro, I too lost the shortcut arrows, as well as the arrow overlays for junctions and symlink.
I finally traced it down to OneDrive/SkyDrive. OneDrive added three overlays to Windows Explorer. Unfortunately, Explorer can only handle a maximum of 15 overlays (if I understand correctly).
Not being a OneDrive user, I went into Group Policy Editor to check if it was enabled. (It wasn't, because I had purposely detached my Microsoft cloud login from my local machine login. But if it had been, I would have disabled it here.)
Then I went into Regedit and found the overlays here:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\ShellIconOverlayIdentifiers
There were three OneDrive overlays listed, and coincidentally, I was three over the limit of 15.
I exported the registry keys for the OneDrive overlays as a backup, and then deleted them out of the registry.
After a reboot, all of my shortcut, junction, and symlink arrows came back, and so far, they have been visible everywhere I've expected them to be.
Just wanted to let you guys know that this shortcut bug/glitch spontaneously got fixed at my end. They all appear now no matter how fast I go to the Desktop after a boot.
I have no idea what fixed it. Maybe after updating my nVidia drivers (to 344.48 WHQL) or something else from Windows Update.