I think something happened to two of them. There were originally 7 but in the opening scenes of Origins and in the loading screen before Hawke enters The Final Seal (to fight Cory), only 5 are shown. Plus there's this mosaic in Inquisition: https://dragonage.fandom.com/wiki/Codex_entry:_The_Mason%27s_Tales:_Invasion
Two of the magisters were removed from the mosaic. Why? Maybe those two died in the fade before reaching the Black City, or in the city itself. Or maybe the other five killed them for some reason. Perhaps they refused to become tainted (Cory implies that they deliberately infused themselves with the taint), which resulted in an argument and then fight, leading to their deaths. Or maybe the process of becoming tainted just randomly killed to of them. The taint tends to do that two people. Or maybe they're still stuck in the city. Or maybe they made it back but died immediately afterwards during the battle with the Archon (assuming that the Canticle of Silence is at least partially accurate).
Anyway, if only 5 magisters survived the events of the Second Sin and its immediate aftermath, that leaves only 2 unaccounted for. One of those two would be the crazy magister who killed and ate another one. And I think the other one was female and became the first broodmother. She would be the queen broodmother mentioned in this codex entry: https://dragonage.fandom.com/wiki/Codex_entry:_The_Eternal_Battle:_Darkspawn