We were taught in Navy training in 1970 that there were no microscopes that could see electrons. That we knew of their existence only because we could hear them bumping into each other. So if they can put that much data on one atom microscope technology must have really improved. Otherwise, why put it on there if you can’t see it to read it.
There isn't "much data" being stored on one atom, there is one bit. For each additional bit stored, another atom is required. What is changed/controlled is the spin of the atomic nucleus, which can be "flipped" by an rf pulse.