The structure of atoms was theorized long before they could be observed with electron microscopes; there is no major deviation from the original theory. And creating atomic bombs depended on splitting the nuclei of Uranium 235 with neutrons; this mechanism is obvious due to its having been observed repeatedly.
The structure of the earth’s core was deduced from studying seismic waves and how they pass through the area of the core. Not as useful as observation with the eye, but not an unscientific start.
True, but based upon so many other things scientists have 'deduced' through modeling, mathematics, and limited sensory data, I wouldn't be at all surprised, that in future, we discover that the cores of celestial objects are entirely different from what has been theorized.