He doesn't dunk the glove in water, pours about a cup of hot water over the glove with the hand stall pointed down. There is a ton of info on this procedure.. Water definitely doesn't hurt leather.Is that the method where he dunks the ball in a bucket of water and beats the snot out of it? If so, keep in mind he does that for pro ball players who don't need their gloves to last. They need it broken in quickly and don't care about longevity.
FWIW, I've used his way of doing it on all of DD's gloves and 2 of mine and some team mates of DD. I also rebuild and relace gloves for those that need it, I'm not an expert but do have experience with gloves. In my observations, it causes no longevity problems. Just my $0.02