When designing the symbol and footprint it is important to know the orientation of the connector to avoid incorrectly connecting it to its mating connector, this is called polarization.
There are 2 kinds of pin polarization:
The pin is not included in the physical model, so it will be missing in the footprint and the symbol.
The pin is on the physical model, but it is closed in the front face of the connector to avoid connections, in this case, the pin will appear in the footprint but not in the symbol.
For example, when looking at the datasheet for this part from Samtec, the polarization option indicates which pin should be omitted. Therefore, the pin won’t be on the symbol and footprint.