If you deem .org to be sufficient and want to use Emacs¹ itself, there is an extension for the zettelkasten method of note taking that you might find useful.

1: Despite originating with the Emacs community, .org files are recognized by many (most?) IDEs, but I’m not sure if extensions are regularly ported to non-Lisp editors.

This is a mandatory comment about Emacs’ org mode since .org files are extremely similar in syntax to .md and can be interconverted extremely easily.