Even in the 1963 adaptation of Shirley Jackson's Haunting of Hill House, the eeriest element of the movie itself is darkness...shadows creeping in at the edge of every frame, threatening to consume Eleanor (along with her slight mental instability and the evilness of the house itself.)
Darkness is terrifying, because the unknown dangers of the world are that much more powerful. It's terrifying, because it deprives many of us of the sense we rely on the most. Sight.
The majority of Nyctophobics are either children, or very old. So, I suppose you'd say this fear strikes those who are most vulnerable. The origins of the phobia tend to be trauma of some sort, which makes quite a lot of sense. After all, night is the main time when children can no longer be watched over by their parents as vigilantly, so it's also the period of one's life where people learn to look after themselves.
The best treatment seems to be what a majority of the phobias I've mentioned is, and that's exposure therapy. Desensitizing the victim to their fears...and medication.
In honor of Nyctophobia, I'd like to share a video I've posted once before in a list of creepy shorts, which characterizes exactly what many children seem to fear the most about darkness...sleep.