Fujifilm GFX 100 has a 102.0MP Medium format (44 x 33 mm ) sized BSI-CMOS sensor and features X-Processor 4 processor. On the other hand, Fujifilm GFX 50S has a 51.0MP Medium format (44 x 33 mm ) sized CMOS sensor and features X Processor Pro processor.
Fujifilm GFX 100's sensor provides 51MP more than Fujifilm GFX 50S'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.
Below you can see the GFX 100 and GFX 50S sensor size comparison.
Fujifilm GFX 100 and Fujifilm GFX 50S have sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Fujifilm GFX 50S has 95% larger pixel area (28.40µm2 vs 14.52µm2) compared to Fujifilm GFX 100, it has larger pixel area to collect light hence potential to have less noise in low light / High ISO images.