Best way of combining textures

I've seen in many games that a lot of textures are used and then applied to same meshes. Some of them are animated so it doesn't seem that they are combined into a texture atlas because it isn't the same when different textures are animated and you have to recalculate all of the uv's all the time. What is more, some of the textures are transparent while most others aren't. Beside, there are very many textures so an atlas would be very big, perhaps too big for Unity to handle. How can it be done in Unity? Do developers break textures into types and then make smaller atlases? Or can it be done with some multi-texture material?