Because when the lights go out there is heavy respiration by all the animals and plants in the tank, but there is no photosynthesis to replenish the oxygen consumed. Oxygen levels, even in nature, drop dramatically and the water near the reef surface becomes hypoxic at night. Water motion helps to bring in oxygenated water and is especially important for animals like corals that rely on diffusion of O2 from the water column. There's actually a thin layer of water that "sticks" to the surface of the corals and becomes especially low in O2 as compared to the overlying water. This boundary layer forms a barrier to diffusion of O2 in and CO2 out of the coral, essentially suffocating it. The faster the water flow, the thinner the boundary layer. It doesn't make sense to increase the boundary layer when O2 is already at it's most limiting.
Essentially none of our animals actually sleep and those that enter some state or torpor don't need lower flow to do so.
Also, many corals extend polyps to feed when light is lower, meaning they would prefer motion to sweep away waste and also get fresh nutrition, near as I can tell. Good question though - great, in fact, since many wavemakers offer a nighttime mode to stop the rocking and rolling.
Also, just because the surface waves may calm down, doesn't mean the currents below the surface have altered by much