Yes, small particles like neutrinos can pass through.
Although to call it completely empty is a bit of a misnomer as well. At this scale we kind of reach the limit of our everyday human definitions, including what words like “empty” means. The space within an atom is “full of” electrons.
You have to remember that the image of little balls orbiting a nucleus is wrong. Electrons are small enough to truly behave like quantum objects, the whole particle/wave thing, are spread out and exist everywhere their wave function allows them to exist. [This is how electrons actually exist around a nucleus](https://en.m.wikipedia.org/wiki/File:Hydrogen_Density_Plots.png). As you can see, they occupy pretty much all of the space, none of it is really “empty”.
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