The nice thing about 3d models is that you can scale them fluently. So whether you model them on fully grown scale and then scale them down or model them as foals and scale them up is left to your personal preference.
However, you might want to take into account that most animals change proportions while growing. Young animals tend to have stubbier legs and larger heads compared to their torsos. Or in other words, younger animals are "cuter". If you want to simulate that, you need an individual scaling factor for each bone of your 3d models.
Another option is to have multiple growth stages per animal and use a different 3d model for each. That gives you the most control over how the animal looks in each stage. That's especially appropriate for animals which look very different in different growth stages (most birds, for example). The aesthetic disadvantage is that animals will go into the next growth stage with a visible "pop". But that clear visual distinction can also be an advantage if it is important for your players to see quickly which animal is in which growth stage (for example if you want the player to look at their herd of cows and to immediately realize "I got 6 baby cows which consume milk, 4 adolescent cows which produce milk and 3 old cows which should have been slaughtered ages ago - why is my butcher not working?").