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.

Nothing makes sense to me Everything seems pointless may seem the same, but have different levels of seriousness and would be used in different contexts. "Everything seems pointless" is much more dire and dark -- "everything is pointless, what's the point of living?" Nothing makes sense to me could be used for something as simple as "The teacher gave a lecture on X but nothing made sense to me." Or "X's reasons for doing Y make no sense to me"