The glass will block UV light. Now if one was to flower with a MH bulb, which youre not, the UV light from MH will increase the oil production of the buds late in flower, so if you were to leave the glass in the reflector, flowering the last week or two with MH would be pointless.
Here is something to think about to help make a decision when there really is no right or wrong. How big is your crop, what square footage does it cover, how tall are the plants, and how bushy are they. With that in mind the distance between the plants and bulb will determine the light intensity that your plant receives; more is better to a certain point. If plants are tall and you leave the glass out, the increased distance of the light will not benefit the lower limbs as much as if the glass was in and the light was closer. On the other hand if youre covering a big area and the light needs to be father away to cover the area, then leave the glass out if the temps are reasonable.
No right or wrong here, people do what they need to do, if temps were low in the tent or room, plants are short and if you feel your plants will benefit from the UV light, leave the glass out. Try Goggling benefits of UV light for Vegging, and then make your decision.
I thought about leaving the glass out and sucking the air from the reflector which would take the heat from the light instead of pushing the air through the reflector and leaving the glass in to remove the heat.