It did affect Cortana. Didn't you see what was happening to her in Halo 3? She was on the verge of succumbing to it and falling into rampancy. But anyways, Cortana resisted long enough until the Chief saved her, but even then her state was very deteriorated.
The same way it did all the Forerunner AI's. If the Flood come into contact with an AI, it will unleash the Logic Plague. It's how Mendicant Bias, the Forerunners most advanced AI, was corrupted and turned against the Forerunners. Granted it took 43 years, but still. If an AI infected with the Logic Plague simply contacts another uninfected AI, the Logic Plague will pass on and the uninfected will become infected. To stop it, communications will have to be cut across the galaxy and only rely on extremely secure connections. It cripples the war effort.
Just like the Mandalorians eventually learned to be able to defeat the Jedi, even in hand to hand combat. The Flood will find a way and they definitely have the numbers to sacrifice to find that weakness.
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