> Well, they're not _plain_ text - there is some markup.

Markup is still plaintext.

> why not HyperText Markup Language?

Why not json or yaml? If you remove the users ability to write the text directly, then why limit yourself to the unstructured mess that HTML is?

> Doesn't HTML have all of these features - hyperlinks, folder structures, "plain" text? Isn't HTML also future proof?

Markdown is human-friendly. There is a whole ecology around using it for those usecases. And you can create HTML from markdown anyway.