The Bohr planetary model, which I assume is what you're referring to, is equivalent to Newtonian mechanics. It's simple to understand and a good starting point for high schoolers. It's even still usable for certain types of calculations.
However, like Newtonian mechanics, at a deeper level and according to modern understanding, it's fundamentally wrong.
Instead we use the Schrodinger electron-cloud model. According to which the ~nucleus~ (EDIT I mean atom not nucleus) is not mostly empty.
It's not pedantic to discuss this, any more than it's pedantic to discuss why Newtonian mechanics is less accurate than relativity.