This is something we've all dealt with: my Hunter is traipsing through Terrokar right now, and nothing makes me more frustrated than hitting those little rivers on my mount and having to dismount in water. When you think about it, the logical reasons for our mounts disappearing once we hit water are pretty sound -- you don't want that cat or wolf you worked so hard for to drown. But on the other hand, it's a huge annoyance -- not only does it slow you down while crossing the water, but you have to wait another second afterwards to resummon the mount.
On larger bodies of water, this isn't so bad, but those little rivers are nothing but trouble (and Gnomes have it even worse). Even cowboys knew how to ford with their horses -- why can't we do the same with our mounts?
Zarhym, the new CM, doesn't seem very empathetic, so odds are that this won't change anytime soon. We can only hope that in future designs, Blizzard stays away from putting the deeper water all over the landscape, where it acts as nothing but an annoying roadblock in front of our next quest. It's not like we don't have enough problems with the water as it is.