Yes it does what ever time you put it on night mode it stores it and will go into night mode automatically at that time
yes thats also why i use night mode, my poor clowns sleep right up against the overflow and i see them at night struggling, so i think they appreciate the night mode. and the flow is raging in there all day so i am sure a little break time is appreciated for everyone. its not like the flow dies down to nothing its just half what i have set, so theres still plenty of flow to keep things moving.
If you keep a high flow tank such as an SPS dominated tank and have fish, then I would use night mode to give the fish a break more so then the pump since our tanks are so small and shelter is not as prevalent. But in a frag tank with no fish, I do not use night mode. I remember reading one time that the current does not die down at night in the ocean.