These links are not seen by the user and let the HTML file link to CSS files (used for styling) and JavaScript files (used to add interactive content).

The static HTML is indexed while links found are passed back to the crawler for discovery. The processor plugs the page into Chrome (version 41 as of now) and renders the content, including ...

So if you want your links to be found, be safe and put them in standard html format. But if you don't want your links to be found, putting them in JavaScript or Flash won't guarantee that.

JavaScript allows sites to customize links in different ways, but doing so may render the link unusable to crawlers. Here’s what Splitt recommends. Do: Keep it Straightforward ...