Pentax 645Z has a 51.0MP Medium format (44 x 33 mm ) sized CMOS sensor and features PRIME III processor. On the other hand, Pentax 645D has a 40.0MP Medium format (44 x 33 mm ) sized CCD sensor and features Prime II processor.
Pentax 645Z's sensor provides 11MP more than Pentax 645D'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 similarity between these two cameras is that both Pentax 645D and Pentax 645Z sensors lack anti-alias (Low-Pass) filters. 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 645Z and 645D sensor size comparison.
Pentax 645Z and Pentax 645D 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 Pentax 645D has 29% larger pixel area (36.74µm2 vs 28.40µm2) compared to Pentax 645Z, it has larger pixel area to collect light hence potential to have less noise in low light / High ISO images.
DxOMark Sensor Scores
Both Pentax 645Z and Pentax 645D sensors have been tested by DxoMark. DxoMark scores camera sensors for color depth (DXO Portrait), dynamic range (DXO Landscape) and low-light sensitivity (DXO Sports), and also gives them an overall score. Of the two cameras that we are comparing, 645Z has scored 101, 19 points higher than 645D.