I do not control my return pump to change. It stays the same all the time. My wavemakers are a different story. I have my two largest Jebaos controlled via my apex and my MP40 through the Mobius app. The other Jebaos follow a random flow during the day and low constant through the dark hours controlled by the on-board controller. The current within the tank varies throughout the day and every 2 hours goes into a "Typhoon" mode as my wife likes to call it.
Regarding the question if the ocean's water movement changes at night versus the day, yes, yes it does. Wind, and as a consequence thereof, waves are generally subdued during the evening. Wind is a direct result of thermal cycling and as there is no sun in the evening to drive this cycle, it generally subsides. Storms and their effect on the reef, both locally and far off, are a different animal.
Reef currents within a pass or on the reef crest/shelf, and slope are partially influenced by wave action locally. Within a lagoon, wave action has a much less influence on currents, in general. The primary driver of reef currents is the tide and that is a result of the moon and its phases/schedule and is as regular and predictable as the tides.
The primary reason I calm my tank down in the evening is to give the fish a break while they are "sleeping", not to necessarily mimic nature, but it just so happens it does, generally...