I'm afraid we have some misconceptions regarding the fundamentals. The following comments are offered in an attempt to clarify the issues.
A negative Joule-Thompson coefficient is observed only rarely - hydrogen and helium gases, and very hot gases (above a reduced temperature of 6 or so). For those who have forgotten, reduced temperature is the ratio of the system temperature to the critical temperature of the fluid (absolute units). Thus, most fluids cool down when pressure is reduced isenthalpically.
The degree of flow turbulence and sudden changes in direction of flow across the valve are irrelevant to the issue here. The enthalpy is preserved, except for heat losses. These losses are negligible, considering that the total surface available for heat transfer to the outside world is barely a few square feet in most valves and, therefore, quite insufficient to allow significant heat transfer by natural convection to the outside air. Recall that convective heat transfer coefficients are also very small.
Finally, huge changes in velocity from inlet to outlet can have effects on outlet temperature arising from the kinetic energy term. Again, these are generally negligible for most real-world valves.
Therefore, the theoretical prediction of outlet temperatures is pretty accurate, as long as you choose the right thermodynamic options in Hysys. In fact, these changes are quite small for liquids that do not show a phase change.
If, on the other hand, the incoming fluid flashes to any significant extent, the valve outlet gets much cooler, as the latent heat of vaporization is being drawn from the enthalpy of the fluid itself. That is why, in the refrigeration business, such valves are called "JT valves".
