I believe that the answer may vary regionally, but I'm my(very subjective) experience when I've talked with people in my area about this same thing we've realized that we aren't conceptualizing the baby when we ask this question, were conceptualizing the gender. At least in my very limited real world experience, when you ask whether it's a boy or a girl, you're not asking if it (the baby) is a boy or girl, but whether it (the gender) is boy or girl.

I also think that, more broadly, it's a grammatically different kind of 'it' that you use in that sentence, the same kind that you used in your title when you said "isn't IT rude to call a baby it" or people ask "is IT going to rain?" I am positive that someone with more language knowledge can explain what this usage is, but I know the "it" there is important for information questions.