The model of the atom all begun with a man named John Dalton. HE had the first comprehensive theory of an atom. He stated that matter was composed of invisible particles. The model of this looked a lot like a marble. Following this model, a man named J.J.
Thomson found the negatively charged particle that science now knows as the electron. He found this through experimentation with charged rays. He fired electrical currents through pipes with gas in them. He notice when he recorded the mass that the mass was not changing. From there he concluded that in the pip contained electrically charged particles.
Next, we had the fine discovery of the nucleus which is credited to Ernest Rutherford. He and colleagues shot alpha particles through a sheet of gold foil. By this the observation was that some of the particles went through, but some of them bounced back. They concluded that this heavy part that the particles could not pass through was the dense central part of the atom. Then they named it the nucleus. Next he splits the atom using alpha particles and nitrogen consequently causing him to discover the proton.
In conclusion the model of the atom was empirically developed because these scientists did not have the technology or the knowledge to see the small atom. Technology meaning they could not see it with a microscope or any means they had at their fingertips. They were ignorant to the fact that atoms contained all these individual particles so that is why they did not have to knowledge for discovering these things. Scientist went through blind experimentation, not knowing what they were going to discover, to develop every existent model of the atom. They did not see the atom they used rays, particles and their knowledge of physics to essentially come up with the idea of every individual particle of the atom and diagram what matter consists of. These aspects of the atom were discovered through observation considering they did not have the logic to discover them and that is why it is empirical.