Steve,
Assuming your question isn't rhetorical
I've used high-top GTX boots (Salomon Quest 4D boots) that are more or less waterproof for 10 years, Here's why: I incidentally chose a pair of boots when I did the JMT in a double snow year in 2011. Those boots were invaluable. Obviously, if you submerge your boot below the top your feet/socks will get wet. My good experience made me a believer in waterproof.
However, I cannot tell you how many times you find a rock for stream crossings that is 1-3 inches submerged you can still step there and stay dry, where you would get your feet wet with any other type of boot otherwise. Further, there were many times where my foot slipped off a log and I'd dip a toe or half-boot and my GTX boots would stay bone dry. They're also really great for snow or mud when sticky versions of either might adhere to the boot and slowly soak it through.
There are cons, weight/breathability namely, but I've been buying the same boot since and I've been very happy with them whether scaling 14ers or grinding out the JMT/HST. I've always been very assiduous in choosing socks so breathability hasn't been a major downside. Thus the Whitney area may not mandate such boots but they've been useful regardless.
What kind of footwear will you be sporting on the JMT?
