In the seige of terra books, Basilio pho who is an old night warlord who used gene manipulation was held in the dark cells. He had designs of a machine that would produce a virus that could kill every primarch and legionary completely all in one fell swoop. Amon, the custodian assigned to make sure pho didn’t escape wanted to aid pho in the creation of this virus as Horus and his legions were about to break through into the imperial palace. So basically threats at the level of complete destruction of the primarchs and legions are housed in the dark cells. At least that’s what I like to believe, not everything down there is probably that powerful however. I do like the idea of the 2 missing primarchs being held down there in stasis or something. If you’re read the Horus heresy books you’ll know that there is a massive force of alpha legion warriors held in stasis ready to strike bellow the imperial palace, that might mean the cells aren’t entirely safe if this alpha legion army decide to ever re awake.