Pentax 645D has a 40.0MP Medium format (44 x 33 mm ) sized CCD sensor and features Prime II processor. On the other hand, Pentax 645Z has a 51.0MP Medium format (44 x 33 mm ) sized CMOS sensor and features PRIME III 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 645Z and Pentax 645D 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 645D and 645Z sensor size comparison.
Pentax 645D and Pentax 645Z 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 compared to Pentax 645Z, it has potential to collect more light on pixel level hence have less noise in low light / High ISO images.
DxOMark Sensor Scores
DxOMark is a benchmark that scientifically assesses image quality of camera sensors. It 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. Pentax 645D and Pentax 645Z sensors have been tested by DxO and the results show that 645Z has a better overall score of 101, 19 points higher compared to 645D's score of 82.