Google's John Mueller replied to a question around links found in JavaScript saying that once the link is rendered, Google will treat the link like how they treat any other link. John Mueller said ...

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).

Google Chrome is getting a new feature that increases security when clicking on web page links that open URLs in a new window or tab. When inserting links into an HTML page, authors can include ...

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.