I am a committer on this project. As of July 20, 2015, evaluated queries are not yet supported. However, the syntax you are using is correct, and when evaluated queries are supported, it should evaluate to a number which will be embedded into the rendered Markdown with the same position and styling as the inline code element.
In the meantime, although it's not quite the same visually, you can create a query block which follows your Markdown block, and executes the same query. This will give you the count in a table, which is less than ideal, but a passable workaround until someone gets around to implementing evaluated queries.
EDIT: The feature has been implemented and works as described.