Let's say that this is the Hive at the height of their power, and the Flood at the height of their power. The first problem is that the Hive have no known biological systems. So let's say that the Flood could infect their Worms. First, the worm's paracausality might render them immune, and second, the worm might be able to consume the infection as it would a tithe. Second, the infection would end a Hive's Sword Logic, and the worm would consume the Hive before anything else could be infected. But even if a Flood infection could take root in a Hive, it wouldn't be able to do anything because the Hive is not alive in our sense of the word. Rather, they exist. Now for weaponry. The Flood rarely use actual weapons, preferring instead to infect their enemies. As this is not possible with the Hive, they must turn to extermination methods. There is no doubt that the Hive have superior ranged weaponry. At close range, the tables would be slightly in favor of the Flood, if both sides had equal numbers. A Hive Ogre could sweep a swarm of Flood, but if they could get into close range, they would thrash it. Another thing is one-on-one matches. A Hive Ogre could easily melt down an Abomination's defenses enough to kill it in melee combat, if not kill it before they meet. Plus, both sides work in swarms, so the Hive could pick off or weaken the Flood swarm before the Flood can actually attack. So, the Hive clearly are better on land, but doesn't the Flood have a super powerful navy? Yes, they do have the capability to infect entire planets. But even if Flood growths cover Oryx's entire Dreadnaught, they will be annihilated once he activates the superweapon. And even if you say that the Dreadnaught isn't that big, or that it can't even move, let me remind you that the Dreadnaught is the size of Earth's moon, and that it can move faster than light due to its reality-warping properties. Oh, but the Dantalion Exodus IV smashed a hole into its hull. That is true. But the Hive let the Cabal on board to sharpen themselves, and the Dantalion Exodus IV actually didn't cause much damage. Remember, the Dreadnaught is the size of the Moon, and the attacking Cabal went into the Trenchway (meaning that they didn't smash through the hull, just fit into a slot), and they just crashed through a few walls inside. Much of the wreckage is just form the Dantalion. But Cabal warships travel at incredible speeds if they choose to, and nothing the Flood have can even come close to that. And all this isn't even mentioning Oryx, Crota, the Deathsingers, Omnigul, or the Court of Oryx, along with Savathun, Xivu Arath, or any other of his countless generals, the Worm Gods, or the war moons. And I've proven that the Hive would beat the Flood with ease without even mentioning how Oryx could Take them all!