The face coverings are worn for religious/traditional reasons and the style varies by country or ethnicity. Frankly, at the age of 3, your son is likely to be more frightened if you project your own feelings about them. I would address it, matter-of-factly, in the context of different national/traditional dresses.
We spent 2 months in Egypt with our then-2.5yo daughter. I was sure that the first time she saw a woman with her full face covered, she would ask me something along the lines of "where is her face". Instead, she never asked and just interacted normally with these women - talked, laughed, played. She sees me at the park talking to women that are covered and thinks nothing of it. There is nothing to fear - they are mothers, sisters, daughters, grandmothers, aunts; doctors, lawyers, scientists, teachers; they get up in the morning, eat breakfast, send their kids to school, even go the beach (yes!), eat wonderful family dinners, and put their children to bed with hugs and kisses. They even have SEX!
We still live in the Middle East and our daughter is exposed to a wide range of head and face coverings - she has never been frightened because WE are not frightened as there is nothing to be frightened about. They are people, perhaps with different traditions and beliefs, but people. Yes, some may be "bad" people, as are some people that are dressed in Gap clothes.
Sorry to sound harsh, but we live in a globalized world, where we have an opportunity to teach our children about so many more things that we were exposed to growing up. Re-evaluate your own prejudices and perhaps you will learn to respect, rather than fear those that are different from you. Frankly, I found your "darth vader" comment to be a bit offensive - you are assuming that the person under the mask is "evil" in some way.
Open your mind, open your son's mind, and we will all live in a better world where there are fewer things to fear, masks and otherwise.