From the example in the Github repo I understand that the JS only compiles the Markdown to HTML. All the content is still being served on the server-side and the client only handles the way it's presented. If I'm correct, I see no reason why it should hurt SEO. All the content is still being crawled.
It's actually the most SEO friendly engine there is because there is nothing but content with Jr.
Actually, you will be missing things like the meta tags for an image preview when sharing the post on facebook and other sites. This still needs to be added.
