It's like the Floods absence has to do with a couple factors. One plausible, and another that isn't an impossible scenario - but very odd.
The Flood that wasn't destroyed by the Arks destruction were contained on other Halo installations, this doesn't exclude Gamma Halo
Second possibility, the Flood aren't dead, dormant, or even contained for that matter; just fleeing from something that might just be a worse phenomenon - and that unidentified ship that landed on Installation 04 is very peculiar.