Marketing books has always seemed to me a very hit-or-miss affair, more art than science, with the reasons given often obviously nonsensical. Some people have good intuitions about it, but I think most theories and reasons given are just rationalization, really.

As for your second point, yeah, in general younger people are much more likely to take gay people for granted, so that seems a particularly stupid assumption on the part of that agent. What I don't know is how much the opinions of the parents are taken into account, as possible buyers of the books. This is a big deal in literature for younger children, but I don't know about YA.

P.