It could be a rank thing, an abbreviation of Alpha one, showing her status at the top of the hierarchy. Or it could be naming her as the original, the creator of all the rest, if your in an ant sort of mind set. It really depends on your interpretation.
I do have a question regarding the white circles on her mask. If she is supposed to be the queen, why does she have A-01 on one of the other panels? I'm only guessing that this is her model number or something, but if she is a Queen, shouldn't she be perfect? Perfect as in, it takes more than one make of a robot to make a perfect design... So, wouldn't the number be higher?