I wouldn't worry about 2' deep puddles, the GX fording depth is closer to 2.5'. I routinely ford streams that deep in mine. I also would not worry about it going up on your hood, that means the GX is plowing into the water and creating a bit of a wake (that actually helps keep water from getting sucked into stuff). The breathers for the front diff, transfer case, and transmission are all plumbed to the firewall and are 3+ feet off the ground to reduce the chance of water ingress.
Regarding the differentials, if you are regularly doing stream crossings/puddles, or if you have not changed the fluid in quite some time, I would recommend a transfer case, front differential, and rear differential fluid change. The rear differential is the most susceptible to water due to having the low-hanging breather. It is cheap and easy to extend the breather into the fuel filler door area with some 3/8" rubber hose and a $5 Toyota diff breather, which is what I have done. That being said, I still get some water in my differentials (but not a lot), as the hot diff hitting cold water can cause it to suck some water in past the seals. I have never seen any sign of water in my transmission fluid, although most GX's would benefit from transmission fluid changes every few years.
The moral of the story it to extend your rear differential breather but still change your TC and differential fluid often, if you are driving through water routinely. My GX gets yearly gear oil changes.