I don't have a wave maker but I do employ that same philosophy with my powerheads. During the day they run at 100% while at night I dial them down to 50%. The reason I do this is because I have a lot of open space under my rock work that gets a lot of flow and I found some of my fish had a hard time finding a spot to rest at night and there were territorial issues that came with that. Once I started dialing back my powerheads my fish could rest anywhere and they were happy with that. This did not seem to affect the grow or health of my corals so that's pretty much how I have operated my flow for over a year now.
In the ocean I would agree that the water movement is pretty much the same night and day. However, in the ocean the fish have a hell of a lot more hiding places that they can retreat too at night. I would imagine that these hiding places would tend to be much calmer than the open water. So if you've got enough rock work for fish to hide and rest at night then you should be okay to run your wavemaker 24/7.
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