I'm not sure if it's a stealth drop-rate change (wouldn't put it past them) or what, but I've noticed the same thing. In the early weeks of 5.3 I was getting on average one pet per run, and had two Stalkers drop in the first few weeks when I was only farming it with two toons. Since then I have killed Vashj every week on those two toons, as well as a few extra times with another toon, and have not seen another Stalker drop. As you said, even the Tideskipper and Waveling don't seem to be dropping anywhere near as often either.
I listed those two Stalkers at an inflated price, not expecting them to sell, but both of them were snapped up within an hour of listing. A bit annoying to me that I now can't seem to replace him for my collection, but I guess it serves me right for being "greedy" - at least the cash went to good use, buying other pets for my collection.