Baking soda or baking powder are used in baking cakes/cookies as leavening agents. When combined with any acid like vinegar, buttermilk etc. it produces bubbles of carbon dioxide that helps your food to rise. This is the main reason why cakes are fluffier than the brownies.

You can bake your cookies without using them, but the cookies would have a very dense texture and they would also be chewy.

Baking soda consumed in a certain quantity (As per the proportionate amount used in baking) is not harmful.