I think it's honestly as common (or almost as common), and about equally disabling (if perhaps more painful, as girls are more likely to internalize stuff).
Asperger's/HFA isn't diagnosed in girls as often because the criteria/symptomology is still based on boys. Girls show different symptoms, that people haven't been trained to look for, that may be less "obvious" because girls tend to be "less outgoing."
I know it never would have occurred to anyone to worry about me-- even though, at 3, I played alone, would not ask for help from anyone but immediate caregivers, and tended to sniff the children in line in front of me. I was quiet, shy, obedient, and clearly good in the books-- these were desirable traits in a girl.
By the time my deficits were A Problem-- around third or fourth grade, when a 30% gap becomes massive and bullying begins in earnest-- I had learned to hide a lot of things. The only obvious symptoms I had, by then, were thumb sucking and quick tears. I don't know about now, but in 1980-something, no one would have dared raise (or consider) the possibility of a highly stigmatized mental issue on the grounds of thumb-sucking and tears.
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"Alas, our dried voices when we whisper together are quiet and meaningless, as wind in dry grass, or rats' feet over broken glass in our dry cellar." --TS Eliot, "The Hollow Men"