You may not want that information revealed for a variety of reasons. Despite the gains in social acceptability of homosexuality, it used to be much worse not that long ago. Many people didn't want their families to know, didn't want it to be public knowledge because it could affect not only current employment but future employment, etc. When determining whether or not you can have a security clearance, they are very sensitive to potential blackmail and if this was something you had been keeping a secret for a long time (before applying for that security clearance) that means it is potential blackmail material. If you were openly gay it shouldn't make any difference because then there would be no blackmail potential but like I said, they likely didn't differentiate and it used to be very common to hide this sort of thing.