That is a difficult question to answer. The siesta approach, which is what this on/off schedule is usually called, does tend to eliminate algae problems. It does this more because of the CO2 than the actual light, though they are connected. CO2 often runs out during the day as plants use it faster than it can be replaced, and when this occurs, the light is useless to the plants so algae takes advantage. The periods of darkness allow the CO2 to re-build, so when the light comes back on, there is again sufficient CO2 for the plants to photosynthesize.
Fish have an internal "body clock" just as we do, called the circadian rhythm, and it is driven by light and dark. We experience jet lag because of this; the difference in the 24-hour light/dark period is unbalanced when you cross several time zones, and your cells need time to adjust your "body clock." Fish have this too, but even greater. You can read more here: http://www.tropicalfishkeeping.com/f...er-fish-81982/
I have not found any definitive data as to whether this "siesta" approach is or isn't affecting the fish somehow. This might be difficult to determine. In your situation, you have 3 "daylight" periods occurring each 24 hours, and that may be pushing the envelope. Two is more usual with this method, though even so I am not confident it is not without effect long-term.