If the Hero wears a mask then the Villain may also wear a mask or not wear a mask, but the Villain's cannon fodder must be maskless. The cannon fodder may wear uniforms to express their loyalty to the Villain and to facilitate unit cohesion. The cannon fodder should certainly be encouraged to express a bit of quirky, comically neurotic individuality to contrast with the monumental visage of the Hero who so clearly embodies unswerving ideals of justice and so forth. A masked Hero gives you more flexibility in terms of casting-you get a recognizable face for the Hero when they are unmasked; and then you have the option of cycling through as many stunt players as necessary-due to injuries, paralysis, death,etc.-for when the Hero is masked.
If the Hero does not wear a mask then the Villain may either wear a mask or not wear a mask, but the Villain's cannon fodder are required to wear masks and uniforms. The cannon fodder must be especially anonymous and conformist when the Hero's beautiful face is boldly displayed for all to see. Also, masked cannon fodder allows you to re-deploy the same ten or so stunt performers over and over again for the big one-against-all battles.
Villains may wear masks to perform a vicious Opposite Day spirit of antagonism when fighting a maskless Hero. Villains may wear a mask to imply some secret kinship with a masked Hero. Villains may go unmasked to play up a spirit of defiance to the masked monumentality of the Hero. A Villain may also go maskless in order to present a charming image to work demagoguery upon hearts and minds all the better to foment a populist uprising against the masked Hero.
Always bear in mind the complexities of masking and not-masking when determining the dynamics among Heroes, Villains, and cannon fodder.