I don’t understand the fixation with creating note taking applications that support markdown. Markdown is a markup language and by definition markup is used for presentation or publishing content.
Markdown makes sense for indicating how you want writing to appear in a published format like a web page or a document. But, do I really need markdown for raw text-based notes that I really am not going to publish? For me marked up content is harder to read.
An example of where I see markdown being used the wrong way is in Noteplan. I can markup my notes for bold or italic but I don’t just see the rendered result I see the markup, asterisks and underlines AND the bold and italic that that is harder for me to read.