I use the flash frequently, when taking pictures of my fish.
If they are in sleep mode then I wouldn't do it, but if they are awake and alert then it shouldn't be a problem.
Since our fishhouse is a building seperate of our home and has natural sunlight due to a clear roof, I find taking pictures best at night with no lights on in the place except right over the tank in question. So I leave a light over those fish to make sure they do not go to sleep before dark.
In your case as long as the fish are moving around and awake it shouldn't bother them.