The "just pretend I'm not here :)" of software development.
It was a conscious decision to mark them as "system apps" and put them on the system partition. They didn't have to do that.
Also note that android apps are more equivalent to plugins or shell extensions than executables. An app can register various OS hooks and callbacks that can trigger behaviour even if no process of that app is running. I'm not sure all those hooks are unregistered if an app is deactivated.