We see a fair few in storage containers and obviously there’s the question of the Endless.
Since it’s implied the entire planets population was sealed away. Does that mean there are billions of them? Considering the human population is only in the tens of billions that’s quite significant.
Given that this includes Covenant species such as Brutes and Elites could part of the Banished plan be to release them to get even more soldiers? Come think of it I am surprised they haven’t tried releasing the Brutes since they’re now an endangered species.
Also, who are all the human cylexes? Why are they under lock and key? Are these supposed to be the original Ancient Humans who fought the Forerunners?
Plus if there’s that many sentient life forms on Zeta Halo, wouldn’t that make a Flood Outbreak extremely dangerous since there’s that much biomass to consume?
Another point. When Cortana is discussing freeing what’s in the Cylexes Despondent refers to them as “the punished can never be freed”. Not the Endless which is a term she later uses when talking to the Harbinger. So are the Punished just another term for the Endless, something different, or a catch all term for everything in the Cylexes. I’d lean towards the later because the Skimmers seem to be a different species to the Endless. So they have been let out and used to bolster the Banished army. It could be that Cortana wanted to “free” the people in the Cylexes because there’s that many of them they are a significant number of Organics that she would be compelled to control and gain access to.
If you have ever played Star Wars the Old Republic this really reminds me of the set up on the Belsavis planet. Where it’s this ancient prison with successively nasty layers of security and the most dangerous prisoners at its heart.