When it comes to thinking, the Zettelkasten solves an important issue which is the problem of scope, which is impossible at the current moment in mindmapping software such as Concepts.
Mainly, Zettelkasten allows you gain a birds-eye holistic view of a topic, branch, or line of thought, while allowing you to at the same time also gain a microscopic view of an "atomic" idea within that thought-stream, therefore creating virtually infinite zoom-in and zoom-out capability. This is very, very, beneficial to the process of deep thinking and intellectual work.