Yes, I remember this riddle from my childhood. I told it to my kids, years ago when they were little. They just looked at me blankly, because of course, Johnny has two dads. I mean, duh? Like the kids in your story, they figured that the answer couldn’t be Johnny’s mom, because that wouldn’t even be a riddle.
I then told the riddle to my husband. He grew up in another country and had never heard this riddle before. He was totally stumped, could not figure out either answer, even with hints… (even though HIS MOM is a doctor!) The kids had to explain it to him.
Other assumptions my kids made (mostly when they were little):
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Somehow, it came up that my husband and I (that is, their parents) were married. My son: “You can’t be married, you don’t MATCH!” At first this was confusing, until we realized that the only wedding he had attended was a gay wedding.
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A story mentioned a male rabbi. The kids complained that the story wasn’t realistic because “a male rabbi? That’s silly!” As it happened, they had only known female rabbis. (Much later, my daughter wasn’t allowed to play a rabbi in a school play because she was female, and as you can imagine, she was irate!)
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Picking up my son from his first day of kindergarten class. “Mom! I made a new friend!” That’s great, I said, then I asked a dumb question (in retrospect), is your friend a boy or a girl? Blank look from my kid. He had spent the whole day playing with his new best friend, and the question had not occurred to him.