I have a young sister who is a ginger and I am a brunette. Sometime I am referred to as "the dark Shires girl" and my little sister is "the light Shires kid".
It is almost certain that the nickname "Dark Annie" comes from her hair.
I am confused as to why people are coming up with such complicated theries as to the origin of her name.
Just to add to Archaic's interesting post, fairness was connected with moral worth and darkness with the opposite9 The 19th century image of Jesus was usually a fair skinned blue eyed man.
Thackeray in his great satirical novel Vanity Fair made the amoral Becky Sharpe a small childlike fair skinned redhead and the good innocent Amelia a brunette, just to reverse this perception.
I had the same question about the use of the term "dark". I can agree that it more than likely had to do with hair color. But for the sake of adding to the conversation:
1. It was a pimp term. For example, let's say Jack McCarthy is a pimp known by the name "Black Jack" McCarthy. So then any prostitute associated with him would be considered "dark".
2. It wAs a perjorative term for the Irish. I remember seeing Dave Chappelle on Conan O'Brien, and he was talking about a show he did in Ireland. He explained how an old Irish man came up to him after the show, and told him how much he loved his act because "the Irish were considered the ni---rs of Europe." Its a horrible association, but saying she was "dark" may have been like Americans referring to some people as "colored".