Hi,
It is ok to use water to calculate the internal volume of the MPX5100AP pressure sensor, just make sure that once the sensor is used for the final application, the internal cavity of the sensor has no residual of water and it is dry, otherwise could degrade the internal gel leaving the wire-bonds exposed and could cause shorts or internal corrosion.
You can probably use a couple of pressure sensors to get the measure of the internal volume of the sensor and use this values for the rest of the sensors without the need of introduce water into these sensors.\
Regards,
Jose