The difference is primarily related to how the coefficients are determined, particularly the calculation of theoretical mass flow rate. The coefficients are the ratio of the measured actual mass flowrate / calculated theoretical mass flowrate. For sonic compressible (vapor) valves, the mass flowrate through the valve is solely dependent on the choked flow in the nozzle. The mass flow rate in this condition is dependent on inlet stagnation temperature and pressure and the nozzle throat bore area - downstream pressure has no effect on the flow rate. For liquid valves, the mass flow rate through the nozzle bore is a function of the square root of differential pressure across the nozzle (inlet minus discharge pressure). Since downstream pressure affects the flow rate, the effects of body bowl geometry fluid dynamics between the end of the nozzle and the exit of the body play a role in the actual measured capacity that cannot be easily captured in the theoretical mass flow calculation. Therefore, these effects reduce the measured capacity and when divided by the theoretical calculation that omits them, resulting in a lower coefficient of discharge.
Body bowl flow dynamics for sonic vapor valves have no effect on mass flow through the nozzle unless the downstream pressure exceeds the critical flow pressure and flow goes subsonic. At that point, body effects start to come into play and you'll notice that the coefficients for sub-sonic vapor valves start dropping to the liquid valve coefficient levels.
JAC