Kellogg's pistol uses .44 rounds, which while slow can still pierce light body armor. Vault suits are mostly leather so it wouldn't have any issue going through; though I was under the assumption that Nate/Nora got shot in the head because Shaun was being held pretty close to center mass and I don't think Kellogg would have risked killing him, too. That and Kellogg aims his pistol at Nate/Nora's head. Don't question the scenario with real world logic, especially when Bethesda/Fallout in general don't, either. Actually, when the SS revives the spouse's pod is sealed and needs to be opened. (Along with all of the other pods, none of which can be opened at all. What a happy coincidence that ONLY the spouse's pod can be opened.) Only the pod with Shaun in it was opened. Also, only life support was disabled. Everyone died but what was keeping them frozen was left intact. The pods were all put into "wake-up" mode, but only the one with Shaun was opened. Once they had what they needed, they reengaged the normal protocol but cut/sabotaged life support for everyone but you because in case something happened to Shaun down the road, they would need a genetically compatible replacement. So they were frozen, thawed, then refrozen.