Some of the mooks are wearing gas masks for whatever reason, and others aren't (usually to denote that the former are elite mooks).
Averted: Not a single gasmask-wearing Mook is encountered by the heroes.
"We need our Mooks to look scary and evil! Like, Nazi-evil! I know - let's make them all wear gasmasks!"
"We only have enough budget to hire ten actors for mook roles. Let's make them all wear gas masks, so the audience won't be able to tell them apart."
Lampshaded: "I don't care if the air's clean, private, you will put on that gasmask!"
Invoked: "Well, truth be told, chemical warfare isn't a real risk; we can't afford it, and the rebels wouldn't do it. The gasmasks aren't there to counter chem attacks, they're to help keep my minions separate from the common rabble."
Defied: "When was the last time outside of drills we had to use these gasmasks? Screw it, I'd rather be able to see clearly."
Discussed: "Do you know why we must wear those idiotic gasmasks all the time? We're not even using chemical weapons! Actually, that's also a valid point. Why are we not using chemical weapons, being all-out evil and shit?"
Conversed: "Why do those villains in video games fancy gasmasks, even if there's no practical reason? I fail to see the point."
Mooks have a hard time running around with those annoying filters impairing their breath and cannot see a thing because of their gasmasks.
A huge chemical attack/accident causes people to hallucinate and think that the people in gas masks are their enemies. The Only Sane Men are the ones wearing gas masks.
The gas masks are all damaged, allowing in some hazardous chemicals.
Mooks still think that added protection and the fear factor are worth it.
Said people are wearing gasmasks because they were behind the accident in the first place.
The gas masks are well-made enough to allow them to see as clear as day and breathe normally.
Played For Drama: The Mooks come from a Death World and cannot take their gasmasks off - normal air is poisonous to them. They are unable to enjoy ninety percent of what galaxy has to offer. Dramatic enough?