Nikon 5400 has a 5.0MP 1/1.8" (7.144 x 5.358 mm ) sized CCD sensor . On the other hand, Samsung NX1 has a 28.0MP APS-C (23.5 x 15.7 mm ) sized BSI-CMOS sensor and features DRIMe 5 processor.
Samsung NX1's sensor provides 23MP more than Nikon 5400'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.
One other difference between these two cameras that is worth mentioning is that Samsung NX1's sensor doesn't have an 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 moire occurring in certain scenes.
Below you can see the 5400 and NX1 sensor size comparison.
As seen above, Samsung NX1 has a 9.6x Larger sensor area than Nikon 5400. 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.