Its not the end of the world if you left the domes in place. You lose some light quality, but its not that huge of an issue. I mean, if you have a dome on it changing the light from natural white to green (or whatever color), why wouldnt you just replace it with a green LED? It will give you the most output because you wont lose any light going through the dome. Also, if you have a partially obscured dome to turn a 360* light into a directional 180* light, just pull the dome and replace it with a directional LED.
But like I said... its not a real big issue if you left them in there.