A paradox then. As the whole definition of it being all mighty is killable. See what I mean? It's running in circles. It's impossible to kill an omnipotent being because it's all mighty, but Shiki can kill that concept of impossibility and definition of all mighty, but the being is unkillable because it's all mighty, but Shiki can kill that concept, but the being is unkillable because.... <- Pretty much what happens.
Shiki's ability completely kills or eliminates the definition you have of an omnipotent being. The whole ''it wouldn't be omnipotent if it can be beaten'' law and definition you hold is killable so if such a law was killed, the being remains omnipotent even if it was killed because your law of ''if it is killed, then it isn't omnipotent'' has no existence anymore. Shiki can alter the rules and laws of the universe after all or recreate everything.
Edit: Just found out [] is an omnipotent being. Whelp, there it is. [] Shiki is omnipotent. Didn't know this 'till now, lol.