It will affect the light. It will also raise the temperature of the tank significantly. Temp in my tank dropped 4 degrees when I took the hood off and installed egg crate instead. Everything I've read said not to use closed hoods on reef tanks because of the heat factor.
How are your lights held above your tank, suspended from the ceiling? Maybe just try raising the lights up a bit.
Are you using a
HOB filter on the tank? I know in my freshwater tanks I can raise the water level to the bottom of the filter and there is no splashing.