Well, it doesn't wash away the good stuff if done properly but so many people have problems with it, I've taken to advising either a polar wash or recrystalization.
My friend has evaporated his ammonia after the wash and it left behind a chalky yellow substance that had no smell of indole and when heated, burned and smoked rather than melted and vaporized. So whatever it is, he doesn't want it in his product.
But it's true as Entropymancer said, that it's not as effective as a polar wash anyway. If you do a polar wash, you need to keep the pH high. My friend tested sodium bicarbonate (pH 8.5), ammonia (pH11), and calcium hydroxide (pH 12) side by side and got nothing from the bicarbonate and over 50% more from the calcium hydroxide than from the ammonia.
STB's do definitely need to be cleaned though. I'm not that convinced that they get lye in the product (the lye comment in my tek was my editor's substitution for "gunk" or "crap" or "shit" or something) but by dissolving the bark, a lot of unwanted material gets into the NP.
I still say recrystalization is the way to go.