Yes. Each atom has an overhead. I measured immediate effect on the scene performances above 40 UI elements. And even simpler: a single atom has overhead. Multiplying atoms has a cost and you need to make choices if you don't want to strain the scene. And beyond that, managing a UI with 100's of buttons through atoms is a nightmare at that scale.
Take a look at VAMStory, it can generate a whole UI on a single atom.