Nothing is not a perception of quantity - zero is a perception of quantity. There is a big difference between zero and nothing. "Nothing" is not something that can exist because it is not something, if you will. It is the lack of existence of anything, if existence is defined as being dependent on that which exists, be it tangible or abstract. If existence is defined as a state of potential, then "nothing" can be the empty state, or the lack of the state of potential altogether. Furthermore, in reference to quantity, the quantity of zero can be present in the state even if it is occupied (and therefore not "nothing") - if the sum of the occupants is zero.
As far as the atom goes, the nothing in that statement implies an empty state of potential, which has a quantitative value of zero. The two coincide, but are not the same. Empty space exists between the nucleus and the electron cloud. Also, if you subscribe to the theory of quantum flux, there is indeed something in the so called empty-space - a myriad of sub-atomic particles (quarks etc.) coming into and out of existence - particles having values such that the net value is zero, but because the particles are present at any given time, there is not "nothing" in this space.
what's really important is figuring out what we mean by existence before we try to decide how "nothing" relates to it...