Go look at the database. There are actually a ton of animals from snakes to scorpions to birds. Some are rather rare and some aren't so easily distinguished from the environment.
Seeing the numbers, you would think you would see a lot more. But given that in real life running around the woods or desert doesn't automatically expose you to the wealth of life in that environment. Animals and their need to either avoid predation and/or the sun (most desert animals are nocturnal), probably makes MGS more realistic than most in terms how readily you will run into animals in the wild.
But I do agree with you that the game in its open worldness lacks something that almost makes the open nature of the game unnecessary. The game could of gotten away with making a bunch of maps the size of GZ and it would almost no different than what it is now. Having permanent Mujahideen or regular Afghan camps, villages and towns around the map that offered something to the gameplay would have gone a long way to justify the game's open world map. The closest thing I've come across in terms of random encounters is catching a prisoner (who wondered off) out the corner of my eye at distance, and seeing him killed by wild dogs before I could get to him.
I honestly love the game but it seems the Kojima spent a significant portion of that 80 million to barely scratch what open world games can offer. They could have used that to make more cutscenes or fleshed out some the more basic mechanics of the game.
I think a part of it is Kojima and his team inexperience with open world titles. This makes me sad because Kojima with one open world game under his belt probably would have made MGS 6 even better, bigger and badder.
Thanks Konami.