The Fans in With Strings Attached. Actually aliens who describe themselves as “kinda lizardy, kinda birdy,” they use default faceless humanoid computer avatars when dealing with the four, and they're never even shown to the reader. Hints of their true appearance come out in their dialogue, e.g., “Ow! My tail!”
Except Jeft, whose brief description by the other two suggests he is a fat Grey with poor hygiene.
Also the god Ardav, who is a bland sexless humanoid who cannot be remembered except as a faceless mannikin.
In the Ben 10 fanfic Hero High: Sphinx Academy, Original Character Spec Masters (as well as his entire family who serve the Tempus) all wear one way mirror masks. It is supposed to reflect the person they serve as a way to prevent abuse as well as to prevent relationships between the two families.
The Watcher and the Deliverer in the Warrior Cats fanfic Golden Dawn: Lost Sunrise. They aren't actually wearing masks or concealing their faces, but those are concealed from the reader by a lack of description of their physical appearances. Why? Because they're both Clan cats who appear in the story (the Deliverer in particular is confirmed to be one of the she-cats in the first chapter), and their true identities are said to be big twists. As well, Aurora, a young she-kit the Watcher is preparing to kill at the end of the prologue, never gets her appearance revealed either.