As another viewpoint in the horses vs. elephants/cows/sheep visibility debate, don't forget that there's little value in killing a horse; their utility comes purely from using them for labor. Cows and sheep you can kill and eat, or use their hide/wool to make clothing; elephants you can eat too or use the ivory for tools, maybe even the hide as well. Not to mention that it's easier to kill them than horses, since these animals all pretty slow (well, maybe not the elephant necessarily, but the payoff is worth it! They must have looked like the mother lode to ancient man).
Now, you can imagine your primative people, lacking much experience or knowledge of the real world and exclusively concentrating on survival; food to eat and tools to use are what they care most about. So then someone has the idea "Well, we use the cow and the sheep for food and clothing, wouldn't it be a good idea to try to get them all together so that we can slaughter them at our leisure, instead of having to roam around hunting them?" And thus, animal husbandry. A similar thing with elephants, though you can use those for labor as well.
Now, once you have the idea to herd your food animals, you might have the idea to try to do this with other animals as well. You see this fast horse creature that has eluded your hunting efforts, or gave little incentive to spend the time hunting them instead of the much easier livestock. Maybe you can use them to get places faster. Why not try to tame them as well? Now that you see a use for those plentiful animals by the river, you can see them on the map. Time to ride them or use them to carry/pull heavy loads.
So that's why you can see cows and sheep and elephants and pigs, etc. to start with; because they're useful even untamed, and horses aren't really. Your ancestors already know what to do with the former; they probably consider the latter to be a pest to chase away (they do eat some plants that humans might want to eat, like oats!). Unless you think the game should show other concentrations of animals that aren't really very useful to ancient man (for some reason, eels come to mind first).
Dun Malg's idea isn't a bad one, but it should be pretty obvious which kind are useful as a food/resource animal, and which kind would have no discernable use. Your ancestors have had thousands of years to figure out what kinds of animals benefited them with their available knowledge and resources.
- - - - - - - - - - - - - -
Now, what this also leads to is some other possibilities for things that should be hidden. Like furs until you get hunting (fur animals tend not to be so great for eating IIRC), maybe fish until you get fishing and whales until sailing. Dyes also seem like they'd at least require some tech, but perhaps the art of dyeing is older than I think. And it's not like you can use them for ages anyway, until you can build plantations. Gameplay concerns are what dictated the hiding of strategic resources, but who's to say it needs to be that way exclusively?