In some early concept art she was blonde. But when they designed her outfit, the artists decided that black hair fits better with the "femme fatale" look. I agree with them.
It depended on how they did it. Miranda was originally supposed to be Scandinavian, and in some of the instances, like where they had her hair up in the concept art, it doesn't look that bad. That said, blonde hair is notoriously difficult to make well in games, and in Mass Effect in particular.
After Yvonne Strahovski signed on to voice Miranda, they scanned her face in, and it turned out she did better with the uniform as a brunette than as a blonde. As well, the Miranda's nationality was changed from Scandinavian to Australian, to better accommodate Yvonne, who is a native-Australian herself. They did run through a few other nationalities though; From what I understand, they tried to make Miranda American at first, then English, then changed it so that Yvonne sounded more natural (this was before she had perfected her accents). Then they changed it again, since Yvonne's actual accent wasn't as sophisticated as they were looking for, so Yvonne did more of a high class Australian accent (There are 3 Australian accents; not regional so much as class or event specific. The first is the one they used for Miranda, the higher class one (think Cate Blanchett being interviewed at the Oscars.) The next is the more general accent, or Strine (think Cate Blanchett on Craig Ferguson or Miss Universe Australia 2015). The last is the stereotyped Bogan accent (aka the Hollywood Australian accent), that is comparable in status to the Texan drawl that everyone thinks all Americans have (think Paul Hogan or Steve Irwin).
I think a lot of it came down to who was going to be modeled. Had it been someone else, Miranda might have been a blonde. The facial and hair structure in the game just accommodated a darker hair color more than a blonde. I don't mind.
Blonde hair and very Dark Brown (raven) hair are my favorites on a woman. Miranda looks perfect as she is.