And regarding the Yiddishkeit questions, there are those with the Emunah Peshuta line.
The mechanchim in our school system are not used to addressing these issues. As you pointed out, these topics are only out in the open in the Kiruv world, and most teachers/rebbeim wouldn’t have a clue how to answer many of the questions that their students may ask. Many of them are parents themselves who belong to one of the catagories that I mentioned.
I really don’t think we can explain the social stigmas you describe with one underlying cause. I believe it is a combination of the above mentioned issues.