I have changed the "Visibility" options, but affected nameplates are still visible/invisible!
AKA How do I hide totem nameplates, trap snake nameplates, critter nameplates, and etc?

AKA Visibility settings don't seem to take affect in combat!

This is controlled by the "AloftVisibility" module (make sure the module is enabled via the "Aloft>Modules" options).

Blizzard does not allow selective hiding of individual nameplates during combat. So, the visibility of nameplates cannot be altered during combat, except in gross terms via keybindings/"Show Nameplates"/"Show Friendly Nameplates" (and their underlying mechanisms).

This means that the utility of the totem/trap snake hiding (or anything that is likely to be created or "appear" during combat) can be somewhat limited. Same issue applies to "critters" (or what you have configured Aloft to consider to be critters) wandering into range during combat, and etc.

As well, some pieces of data used by Aloft to characterize nameplates for visibility purposes can only be obtained via mouseover or target action (i.e. pets and their owners, creature types, etc).

If the nameplate of a friendly player is visible when they join your group, their nameplate may not be affected until you leave and re-enter visible range.

If things are not being hidden in the desirable way, the main workaround is to enable the AloftAlpha module, and configure the Visibility settings to use nameplate alpha to control nameplate visibility (Blizzard allows nameplate alpha to be modified in combat). The nameplates are still "there", and can affect click-through in crowded situations, even when not visible. But this will at least get them off your screen. Another possible workaround (if you are not in combat) is to toggle (or "bounce") the visibility of nameplates using keybindings (or via "Show Nameplates"/"Show Friendly Nameplates" as appropriate); turn all nameplates of the relevant type (neutral/hostile, or friendly) off and then on again, or on and then off again, as needed.