When I ride at night I usually stick to residential streets due to the lighting factor. I live in the Richmond (north of GGP) so I ride Cabrillo out to the beach, then climb up the hill to Geary and back down Clement to Arguello. I tend to focus my night rides on climbing hills. I will also cut through GGP and ride around the Sunset.
Parts of GGP are fine at night; JFK drive, west to the De Young museum/Academy of Sciences, for example. Many times the streetlights farther west are broken or turned off so you need some serious headlights, otherwise there is a very good chance you will crash. Some of those roads are poorly maintained and have huge potholes, roots pushing up, etc.; hazardous enough in the daytime, let alone at night.
The Great Highway is pretty well lit if I recall correctly, and a nice long straight stretch. There can be a crosswind from the beach though, and the west side (southbound lane) can have sand drifting across. That can be treacherous. I prefer to ride on the "old" Great Highway (on google maps it's called "lower great highway"), which is one block east of the Great Highway. I take that down to Sloat and head east to the West Portal area, then head north through the Sunset.

There are plenty of options though, I just tend to stay on the west side since it is closer to home and much quieter in terms of traffic. Hope this helps.