David,
It's not my assertion, it's how the thermo textbooks define a Joule-Thomson process. The assumption is that no work is done by the fluid in expanding, but heat transfer DOES occur (thus JT refrigeration processes). I'd guess that would take a certain length of line (or a hx) to allow the fluid to reach thermal equilibrium to its surroundings, and thus approximate a JT process.
You are correct that a typical orifice or nozzle expansion flow is better fit by an adiabatic or isentropic model (no heat transfer), and that may be what a JT valve looks like if you measure the u/s and d/s temperatures close to the valve. Dunno, never used one.
Finally, "my assertion" (the textbook's actually, via wikipedia to Sonntag & Wiley) included the italics (mine) that it was for an ideal gas; the OP never stated what he was using (natural gas) until after my post; you are correct that real gases, especially polyatomic ones, can/do have non-constant Cp.