I think attractive female villians probably outnumber the males, but is it entirely a one-side thing? It seems to me that everything from Shakespeare to pulp fiction has both male and female villians that are attractive in a transparent way that beguiles and fools only the opposite sex. Members of the same sex can see right through the act.
For example, The character, "Dracula" (With the exception of Nosferatu) is generally depicted as a wealthy, powerful male that is irresistible to women for some reason.
Glen Close has been mentioned for her portrayel of 'Alex Forest" in "Fatal Attraction" but I think in fairness, it should be pointed out that she also played 'Teddy Barnes' a female character that get's taken in and seduced by a male villian (Jeff Bridges) in "Jagged Edge"
The movie "Deceived" with Goldie Hawn and John Heard is faintly similar, only in this move the protaginest finds out she's married to the villian.
Despite being dressed frumpily, especially when compared to the "Good guys" the "Agents" from the "Matrix" trilogy aren't physically deficient. They're depicted as cold characters, --but then so was the Snow Queen from Narnia.
Maybe I'm "reaching" here because like many men, I honestly don't know what women find attractive. (Or why) I have noticed though that the, "Phantom" from Phantom of the Opera has gradually been morphed by Hollywood from a horribly disfigured character into one that seems handsome in all except that which can conveniently be hidden by half a mask.