All electrons can “see” are other electrons; that is to say, no electron can peer into the nucleus to see its structure. So electron microscopes can make very crude images of molecules, but you literally can’t “see” anything smaller.
The o.p. has a number of misapprehensions (such as the electrons physically orbiting the nucleus at high speed, or that the space in atoms is “empty”), which is not his fault but an artifact of the extremely faulty methods of conceptualizing and teaching basic science in general education. Suffice it to say that fundamentally what you think of as particles are actually distributed fields that interact at a point that is determined statistically at the time of interaction, following a set of laws we call quantum mechanics (as distinguished from classical mechanics). Some people would call this “collapsing the waveform” though there is no evidence that there is any physicality to this business of collapse; it is considered a mathematical formalism that is used because it works.
The same is true for the rest of atomic and subatomic physics; we have mathematical models that invoke things like composite bosons like protons and neutrons, made up of quarks, electrons, photons and other “gauge bosons” that “carry” force interactions. To make this more confusing, all of these particles have at least two generations of particles that have similar properties but are heavier and highly unstable, appearing only in the highest energy interactions in cosmic rays entering the atmosphere or particle accelerators. We can’t “see” any of this; instead, we take our existing model for particle physics (now unimaginatively called the “Standard Model”), look for holes in it, work out what sort of properties a particle would have to fill those holes, and then run particles into targets or each other at fantastic energies until we get decay products that match our predictions.
If the whole thing seems like a bit of a Ponzi scheme, well, you may not be terribly far off. Elegance and economy has been a guideline to identifying credible theories of physical mechanics, and the elegance and symmetry of Newtons laws of motion and gravitation and Maxwell’s equations of electrodynamics have proven out the value of such an approach. After a couple decades struggling with phenomena at the extreme of speed and gravity, special and then general relativity settled down into a very precious and useful theory that has been almost universally adopted (albeit, without still providing a fundamental answer to what “spacetime” is). But quantum mechanics and the Standard Model is a ghastly, cobbled together theory for which the primary (and perhaps only) virtue is that it works, or, at least works well enough for any practical purpose. Attempts to join quantum mechanics to other theories like electrodynamics (called quantum electrodynamics) have resulting in a generally usable theory only by taking some pretty large leaps across formal proof.
I think most physicists who stop to think about it believe that there is some further, deeper set of mechanics that are fundamentally more elegant, or at least, not as ugly as a warthog at a prom, but aside from vague and sometimes mystical ramblings about things like “the implicate and explicit order” or how Buddha had quantum mechanics figured out even though he couldn’t calculate a parabolic trajectory, no real explanation has emerged.
So, to get back to the question of the o.p., scientists know what they know about the structure of atoms by making up some wack-ass theories, throwing them up against the wall, and running experiment after experiment to see which ones stick, and then assuming that it all means something that, if not sensible, is at least consistently repeatable.
Stranger