Fujifilm X-E3 has a 24.0MP APS-C (23.6 x 15.6 mm ) sized CMOS X-TRANS III sensor and features EXR Processor III processor. On the other hand, Nikon Z9 has a 46.0MP Full frame (35.9 x 23.9 mm ) sized Stacked CMOS sensor and features Expeed 7 processor.
Nikon Z9's sensor provides 22MP more than Fujifilm X-E3's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Another difference between these two cameras is that Fujifilm X-E3's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moiré occurring in certain scenes.
Below you can see the X-E3 and Z9 sensor size comparison.
As seen above, Nikon Z9 has a 2.3x Larger sensor area than Fujifilm X-E3. Larger sensors give photographer more control on the depth of field and blurry background compared to smaller sensor when shot in same focal length and aperture.