I definitely believe that it does. Whether you're a programmer or not, markdown is SIGNIFICANTLY faster to write than actual HTML code, and when the purpose of using a templating system like this is often to reduce the time required getting things to look good. By understanding markdown, the time required to make a presentation will be reduced significantly.
Alternatively, you could write a presentation compiler that translates Markdown to the appropriate deck.js HTML. You could even make it support different presentation frameworks, maybe even LaTeX/beamer.
No it does not.