Optical density of glass is 1.5 ish, optical density of water is 1.33 and air is 1.003, but because the thickness of the glass is so small it isn't a huge amount of light lost.
Nor really but as stated above if the glass gets dirty it can start to block out some of the light. Also it might depend on the type of light you have. A higher watt light will be able to go further then a low watt light. A peice of glass is always good betwen the light and tank to keep water out of the light.
As i side note....... as of late I removed my class cover....result...has kept my temperature down (no chiller) but my evaporation has gone up. My initial concern as the same as yours (diffusing the light). Others say that removing the cover aids in water-air-gas exchange. I cant speak intelligently on the subject. My LFS guy says simply water and eletricity dont mix so keep the cover!!