That mainly happens if have it flushed by a high-pressure machine, which is what most garages will do. There's the possibility that gunk in the transmission actually seals certain areas, and removing the dirt may cause it to leak.
A clean transmission is not necessary a good thing, but clean fluid is quite important. As the fluid goes through many, many thermal cycles and years of usage, its chemical properties will begin to degrade. This is what causes slippage, poor shifting (sometimes), and just general bad performance. Keep in mind that your engine transfers power to your automatic transmission by propelling fluid at a very high rate of speed.
Dropping the pan will only remove the few quarts inside the transmission itself, leaving quite a bit left in the torque converter. Changing the fluid in the pan is generally enough from a maintenance standpoint, and is the same way that I prepped my XJ after I bought it (93,000 miles).
If you want to change as much fluid as possible, you can do a "low pressure" flush. Basically, this involves removing the transmission lines that run to the radiator, placing the inlet into a vat of fresh fluid and the outlet into a waste container. Start up the engine, put the transmission in gear, and let it pump out the old fluid and suck up the new stuff. When you see new fluid coming out of the outlet, you can replace the hoses. Just be sure that you don't run out of new fluid! This method ensures that the fluid is only pumped through at pressures the transmission will see during use (as you're using the tranny pump itself), reducing the possibility for dirt to become dislodged.
