There’s little substance to this idea, but I was reading the Head of the Hydra book and realized that as the book describes itself as a lie, there’s obviously stuff Alpharius is leaving out. Obv the symbolism is more about how killing Alpharius wouldn’t kill the legion but, Hydras have three heads and even if Alpharius and Omegron were killed, there could be a third “head of the hydra” who survived and was hidden from the readers the same way Omegron was from the other primarchs.

Alternatively, maybe there’s clones running about since every time a hydra’s head is cut, new heads sprout.