In writing a HDM fusion of my own in another fandom, I discovered that apparently in an interview Pullman said that he doesn't quite know himself why some people have daemons of the same gender, but that it may indicate some particular gift like second sight (hence why it's so rare). Which I find pretty cool, myself, and makes more sense than same gender daemon = gay, for mostly the reasons you've cited above.

Long live Wikipedia. *grin*