Anyone know where the Hidden Message Settings are stored in the registry?
They aren't. These are saved in the FixedProfile.aws XML file:
C:\Users\
USERNAME\AppData\Roaming\Autodesk\
AutoCAD Product\enu\Support\Profiles\FixedProfile.aws
under the Profile\StorageRoot\AcApData\HideableDialogs section.
Here's a pic showing this in XML Notepad