It’s more appropriate to say that atoms are mostly almost-empty space, with some areas of less-empty space.
Remember, at that scale, particles don’t hang out at specific points. They’re fuzzy clouds distributed across regions of space, in the sense that they are more likely to be in some areas than others. It’s true that atoms are much larger than the particles that make them up, but “empty”/”not empty” isn’t a sharp distinction the universe actually makes. Even the deepest vacuum isn’t totally “empty”, it’s full of the same fluctuating fields whose bumps we call “particles” (or to interpret this another way, particles are constantly appearing and disappearing even in high vacuum). An analogy here is that even a very calm ocean is moving and flowing, even though “waves” as distinct objects are mostly noticeable along the shoreline.
Atoms aren’t “solid” – that notion only makes sense for collections of atoms. It’s better to say that atoms are kind of “squishy” (in the sense that one atom can’t easily enter space very close to another), but that it takes quite a bit of force to squish them by very much. They’re opaque because their electrons interact with light – remember, opaque doesn’t mean “physically blocks movement”, it means “light can’t pass through”. At that scale, light is “as big as” anything else.
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