I think that zoos will live on for a good long while. Seeing a animal in VR/AR doesn't give the same feeling/appreciation for animals as seeing one does. Also, it will take a while to make a lot of species anatomically accurate, as they most likely can't reskin a ton of animals, as well as there being over thousands of species displayed in captivity, and a game can't simply replace that amount very easily. So ABCs will most likely be made first, and if lucky we get more animals that aren't that known. I don't fear that in the course of our lives zoos will disappear because of this because it takes way too long to make something good that will be able to fully replace a zoo visit.
The only fear I have regarding VR/AR zoo simulations replacing zoos is the loss of recognizing certain species, as in, forgetting to give them appreciation via this method. Because, why would we make 100 species of lemurs (according to wikipedia). I also think that zoo visits can be seen as theme parks, it's a nice day away from home, the stress and whatever you got going on for issues. And I definitely do not think that a VR/AR experience can replace that.