I never understood schools or anyone hiding something this significant from parents. If the parents are abusive, then department of family services, police, courts can play their role. It isn't up to the school to decide this.
I enjoyed talking with parents and sometimes surprising them with what I saw from their kid (a quiet kid became an active leader, a troubled youth giving good advice to a younger scout, etc). It was one of the joys of the job to surprise parents by sharing what was going on, sometimes some tough conversations, .... I can't imagine hiding something from them.
About 1.2 -3% of youth are trans, so let's go with 1.2% and assume the rate is half of that in BSA ... So 650,000 youth * 0.6% = 3,900 trans youth. I would up guess many trans avoid scouts.
Gay youth are 7-9%, assuming that number holds you probably have 50,000 gay youth in BSA.