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.