In order to turn on numbered-sections in latex output you need to use numbersections in your YAML block. If you ever want to “discover” things like this with pandoc just poke around the templates:
$ grep -i number default.latex
$if(numbersections)$
$ grep -i number default.html*
$
As you can see this option does not work with html.
Markdown and YAML I tested with:
---
title: Test
numbersections: true
---
# blah
Text is here.
## Double Blah
Twice the text is here
If you need it to work with more than beamer,latex,context,opendoc you will need to file a bug at github.