What kind of led light is? In my experience I have found that the shimmer gets better the higher you have your leds (to a point). Cant really comment about the performance without knowing what kind of fixture it is.
The answer is yes. You are losing performance by having the light shine through a 2nd medium. Glass tops are nearly never salt or moisture free and are generally not made from the clearest glass. How much performance you lose is dependent on the combination of how the three above stated variables react with each other.