Yes, but that doesn’t mean you’re protected from other players. If there’s a way for another player to enter your base, they can kill you. Even if they can’t enter, they might be able to shoot you through a window if you’re logged out close enough to one. Or if you’re logged out close enough to a wall, they could throw up a noxious gas cloud (using a gaseous orb or a poison arrow) right outside your wall and kill you that way.
Point is, you should check your event log to see how you died.
That’s for your base. If your animal pen wasn’t placed on foundations that are connected to your base, then it didn’t share the decay timer with it. That’s why I asked if you knew how the decay timers worked.
Let me dig up one of the posts that I wrote to explain it and I’ll link it here.
EDIT: Here’s a detailed explanation of the decay timer mechanics, to the best of my knowledge: