The hive have structure though, a society behind them. The flood are just super zombies. Flood would never do something like hollow out the moon to make a cool man cave for their demi-god. Stuff like that takes time, and the hive love to take it slow. How long was crota chilling in the moon not invading earth? If thats how hive conquer new territory its no wonder it took them a thousand years to reach their current status. In the end the hive are smart, have magic, have organization, and gods who can only die under specific circumstances which the flood would struggle with.