There’s no way to see what files are available in a gist, when listing a user’s gists. So using a file to hide a gist wouldn’t be possible without fetching the gist (which is expensive, even though they are cached in-memory). You could use a file to customize the display of an individual gist, but so far I’ve hesitated to make
bl.ocks.org more configurable than necessary. You can hide individual files in the source view by using the prefix "README"; also, large files are automatically not shown to prevent the page from hanging during syntax highlighting.
Mike