There's something odd about Authors Say Agents Try to “Straighten” Gay Characters in YA « Genreville. It's not hard to find gay characters with prominent roles in YA. People have made lists:
Poking Badgers with Spoons - Science Fiction and Fantasy YA novels with Major LGBTQ characters
megwrites | Don't mind me and my big gay book spam!
Now, I've been lucky in my career, so maybe I just haven't run into the homophobes who would've told me to de-gay "Secret Identity" or Elsewhere. I would love to know if Francesca Lia Block faced obstacles selling the Weetzie Bat books, or if anyone told Holly Black to de-gay her work.
In my experience, understanding publishing is easy: it's a business. The notion that YA publishers don't want the next Holly Black is very, very strange.
ETA: The story is more complex: failfandom: essential update on the Rachel Brown and Sherwood Smith story