Should I remove Cmagnet base for installing glass bed?
The more layers, the higher the temperature you need to set the heated bed to reach the same print surface temperature as before (air is an insulator, so when entrapping air between your layer you insulate the heated bed). 

I do not know the weight of the magnet base, but, keeping adding weight is not a very good idea unless your bed goes up and down (movement in Z direction is generally much more slower than in Y direction), but the Enders 3 bed goes back and forth. The more mass the axis needs to displace the less accurate the print.