SystemUI.apk is an System app which needs to be always running to provide the Android UI as you know, like Navigation bar, Status Bar, even Wallpapers, and lots more ....

It's a very bad idea disabling it. Even if you disable it, it'll just restart.
If you remove it, your phone won't be having an UI.

How can it both be running and be disabled at the same time?

As far as the question is concerned, I think the current instance of the app will be running eventhough you disable waiting for the effect to take place on reboot.
But Android may not allow SystemUI being disabled during boot, by forcibly starting the app and its services.

If you are a developer/debugger and really want to disable it for some reason, this might help: http://stackoverflow.com/questions/28055413/can-i-disable-systemui-from-within-my-android-app

I think you can also Freeze it using apps like Link2SD :)

SystemUI.apk is an System app which needs to be always running to provide the Android UI as you know, like Navigation bar, Status Bar, even Wallpapers, and lots more ....

It's a very bad idea disabling it. Even if you disable it, it'll just restart.
If you remove it, your phone won't be having an UI.

How can it both be running and be disabled at the same time?

As far as the question is concerned, I think the current instance of the app will be running eventhough you disable waiting for the effect to take place on reboot.
But Android may not allow SystemUI being disabled during boot, by forcibly starting the app and its services.

If you are a developer/debugger and really want to disable it for some reason, this might help: https://stackoverflow.com/questions/28055413/can-i-disable-systemui-from-within-my-android-app

I think you can also Freeze it using apps like Link2SD :)