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In the story itself, I don't think Aldnoah is any particular thing, but rather the name of the ancient Martian civilization.
As for the title, "Aldnoah" is the name of the overall franchise and "Zero" is the title of this particular season, just like Fate/Zero, /Stay Night, etc., or Selector Infected and Selector Spread Wixoss. Given Urobuchi's involvement, "Zero" is probably being used in the same sense as Fate/Zero.
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