No; they do not have the same meaning, but they are related. Usually, when you say "nothing makes sense" it means you do not understand. When you call something "pointless" you mean that you do not see any purpose for doing it. Doing something pointless would be a waste of time. For example, "The teacher gave me the pointless exercise of copying the sentence 100 times. It made no sense to me."
In this case, you saw the exercise as a waste of time and you didn't understand why the teacher told you to do it.