That's a good question. There are cases where the dependencies in Rmd files are not important; they only matter if you're deploying a directory of R Markdown files rather than a traditional Shiny app. For the latter case users might not even have knitr installed and could have inconsequential Rmd files somewhere in the directory structure (though this seems like it will be relatively unlikely). 

The most correct thing here would be to mirror the logic in Shiny Server with respect to determining whether the directory should be served as a Shiny app or as R Markdown, but I'd sooner be conservative here than rely on that logic staying in sync.