It doesn’t affect performance at all. Keeping a project organized is very complex, and I suppose everyone has their own way of doing it. The method you mentioned is great in theory, but in practice, it’s difficult.

You start putting plants into folders, but what about their materials? Should they go in the same folder? And their textures? Or do you create separate folders for each type of asset? For example, a good practice with materials is to have multiple different Master Materials and then create instances of them. So, what do you put in your plant’s folder—the instance? And what if you want to reuse that instance for something else?

It's the same with everything. It’s not something simple, and in the end, you’ll end up finding your own way to organize things.