It seems to me that spectral little girls are used much more often, therefore they are seen as being scarier in some way? Accurate?
Ghost girls. They have boo-bies.
This is a total WAG, but I think the reason girls are used more than boys is the same reason ghost kids are used so much. Kids are supposed to represent everything innocent and sweet; since ghosts are scary and grotesque, a ghost kid is that much more horrifying (because it’s innocence made into something terrible). Since young girls are sometimes considered more “pure” than young boys, it might be more effective in scaring or terrifying audiences.
Feel free to tear this theory to shreds.
I won’t be doing it because I generally agree with it. However, I would also add that little girls are used more often because they appear harmless at first glance. That way you initially get the audiences’ or readers’ to underestimate the threat the character poses.
People picture young boys as being rough or mischievous. Little girls are seen as safe and cute. I think a ghost little boy would bee seen as pranking or naughty.
I’m not saying that the perceptions are anything close to reality, but I think there are baseline assumptions that our culture makes.
Those twins in The Shining.
::shudders::
Ghost Dads are pretty horrible, too.
I agree - and yet I don’t. Girls are spookier than boys, for a couple of reasons.
Girls are (or were when I was a kid; things may have changed since the late mesozoic) much more likely to be into seances, pseudo-mystical games (“light as a feather, stiff as a board…”), fortune-telling, etc., while boys are busy running around butting heads and stuff. (Obviously this is a gross generalization, I’m sure there are former tom girls and Wiccan boys on this board.) So it kind of makes sense (in a horror fantasy context) that a girl, being more likely to be engaged in spooky, supernatural stuff in life, would be more likely to be engaged in spooky, supernatural stuff afterward.
Also, most screenwriters and horror novelists are, I believe, male, so females (of any age) are simply more of an enigma to them.
I love you.
If you’re hawt, I can be had. 
Ghosts are scary because they have powers that can kill people if they get careless or angry. Child ghosts are less rational, and more likely to lose their shit and kill someone. Girl ghosts, being female, are even less rational, and therefore even more dangerous.
Ducks and runs
Unless there’s obvious signs of abuse or neglect (see Toshio in the Ju-On/Grudge movies), boys don’t trigger the protective instincts quite so hard as girls, so you’re less likely to end up with ‘oh, you poor dear, do you need help? Aaah, oh my God, get it off me!’
Girls for sure, same as real life.