Can elementary particles (like the electron, photon, or neutrino ) go through an atom (not the nucleus)?
It depends on the probability of interaction. This probability is computed using Fermi's golden rule, and it involves the strength of the interaction and the number of allowed final states. Weaker interactions means higher probabilities of going through the atom. Some examples:
- Neutrinos only feel the weak interaction, so their probability of going through the atom is almost exactly one.
- Neutrons don't interact with the electronic shell, but do interact with the nucleus via the strong force (this is how fission reactors work).
- Photons can be absorbed or produce stimulated emission if they have the frequency of a spectral line. Energetic photons can also suffer photoelectric effect, Compton scattering, pair production, etc.
- Protons, electrons and $\alpha$ particles have electric charge, so they will interact electromagnetically with the atom. The probability of going through increases if the particle goes faster.
Notice that I've talked about probabilities. As far as I know (correct me if I'm wrong), there's no known particle that has a zero probability of interaction with electrons and/or nuclei. Sometimes they will go through, and sometimes not.