Do glass shelves affect sound Quality?

The answer is yes, but exactly how much and whether it's bad is debatable. Glass has a bad reputation among some audiophiles. You'll find comments about ringing and glass adding a hardness to the sound of components. In the past I've used glass and didn't have any problems, but I was using fairly thick 1/2 inch slabs. If you want to experiment I would suggest starting with rubber or cork type footers to see if you notice an improvements in sound quality.

Agree with Onhwy61. I've always avoided glass but how much it deteriorates the sound would be hard to judge.