I've found depending on your lightning t5 or stronger will trap in a lot of heat. also doesnt light reflect/refract or w/e when it goes through glass? wouldn't you be loosing PAR/spectrum etc.... i could be wrong but w/e asking doesnt hurt =P
I have to have glass over my tank otherwise I get salt spray on my MH lights. Temps can run high, and you have to be careful and make sure that you keep them stable.
I havent noticed any loss of coral growth, but maybe that is because my tank has always been covered.
My tank also is not completely covered, just glass underneath the lights...probably 3/4 covered.