Why do conductors have a positive charge, a lack of free electrons, not as excess number of protons?

The quantisation of electric charge, q = ne, applies to electric charge only, even though charge cannot exist without mass.

One simple rule to think here is that electric charge is a scalar quantity with magnitude. It has positive and negative signs, depending on the direction it is forced to move in an electric field. Mass is always positive. So when you add mass, it never cancels out or becomes zero. Also do consider that a charge can never exist when there is no mass. In calculations, you must remember not to take in the mass but just the charge itself. 

No, there may be some charges inside the system. The overall charge is zero because the total positive charge will cancel out the total negative charge inside. This directly follows the principle of additivity of charge, where the positive and negative charges are the algebraic sum of each other. 

Even though charge cannot exist without mass, we can only have the quantisation of electric charge using the equation, q = ne. We look at the number of point charge and the electron's charge. 

One rule to think here is that electric charge is a scalar quantity. It has magnitude. It has both positive and negative signs, based on the direction it is forced to move in an electric field. Mass is always positive, on the other hand. So when you add mass, it never becomes zero.