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If you currently have the ability to see hidden categories, be aware that you could lose that ability. Do not under any circumstances chose to "restore all default settings" in Special:Preferences, as this will clear the ability to see hidden categories. There is no way to re-enable this feature — not even by making a request of Wikia Staff.
This same advice presumably holds for any other feature that used to be in Special:Preferences but was recently eliminated when the list of options was severely curtailed.
This message is likely not significant to any users who started using Wikia in the last six months, or those who never enabled hidden category viewing in the first place.