I'm actually a bit curious as to how many of the people who have posted in this thread have actually used airbags with a WDH. Or airbags at all. But I digress. :-)
You want to measure the rear unhooked height so that you don't air the bags up so much that the rear actually sits HIGHER than stock unloaded.
As far as measuring when not using airbags, I still think it's a good idea. Why? Because I like all the data I can get - and it is good to know how much sag you have both before and after WDH setup and such.
Getting scale weights will give you more definite numbers than fender height measurements. Sometimes, especially on heavy duty trucks, sag isn't as easy to measure due to heavier springs and such. But gravity doesn't lie and will give you true numbers on what your WDH is giving you.