Whether there will be ill effects or not probably depends on how dirty the filter is and whether it is open (e.g., an HOB) or closed (e.g., a canister).
When turning off a canister for an extended period of time, I'd worry about the canister going anoxic, especially if were very dirty inside. Turning the canister back on would expell stale water with little or no oxygen content into the tank. I doubt you'd get much action from anaerobic bacteria producing hydrogen sulfide gas (the rotten egg smell associated with a gas that can poison your fish), although I don't know that for a fact. I would also worry about ammonia & nitrite levels rising in the water column for the period during which the filter was off. Depending on the stocking level, I'd also wonder about oxygen depletion in the water column.
With an HOB filter, I think only the latter two concern would be valid.
In any case, many, many fish come from waters where there is constant movement, so they generally are well adapted to it.
Do you have some specific reason to fear your fish are being harmed by current at night? If you are, you can fashion a refuge from currents behinds plants, rockwork, etc., where the fish can hide out if they don't want to deal with the current.
HTH,
Jim.
