Yep, he was. If it was not the case, in the Devil ending it wouldn't be Saburo's engram who V speak to. So yeah, Saburo it well dead in the heist, by his own son, Yorinobu.We can almost conclude with certainty that it wasn't Saburo's clone that was killed in the Heist
His engram is "alive", but he don't drink quietly a coffee somewhere, he's "stuck" in Mikoshi (like all the other engrams) since Yorinobu became the "Arasaka's emperor" and closed all the access/infos to anyone, even to his sister, HanakoHow do you know he didn't? Arasaka has secret facilities all over the world and Soburo could have a backup storage somewhere with an Engram ready to be integrated. It's only a few weeks from the day he dies to the end of the game, he could be sitting somewhere sipping coffee and waiting to see how things play out.
And for recall, the Relic (prototype) have never, never worked before V. No human have never survive to the process. If it was the case, for sure, Saburo would have already been transferred to a younger body...