Keith's answer didn't work for me out of the box. The only thing that took to the registry value modification was ShowSuperHidden. Both the Hidden (Show hidden files...) and HideFileExt (hide file extension) reverted back to their previous values as soon as I opened the View tab in Folder Settings.
Here's my solution, which I found after some trial and error (explorer.exe is automatically restarted):
$key = 'HKCU:SoftwareMicrosoftWindowsCurrentVersionExplorerAdvanced'
Set-ItemProperty $key Hidden 1
Set-ItemProperty $key HideFileExt 0
Set-ItemProperty $key ShowSuperHidden 1
Stop-Process -processname explorer
I tested this on Windows Server 2008 R2 and Windows 7.
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