There is nothing confirmed, but there are a lot of possibilities.

1. Darkness is a status effect in Final Fantasy, which is also known as Blind. It makes the affected miss their attacks. So her nickname could be a reference to this.

2. It could refer to her masochism, her inner "Darkness"

3. It could be a slightly modified Dustiness. 
Dustiness in Japanese is ダスティネス. Darkness is ダクネス.

Keeping the first katakana and the last two of Dustiness, changing the "su" ス into a similar looking "ku" ク and discarding the other two katakana, and you have Darkness.