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 ...

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 ...

Always test your pages using Google’s own tools and third-party resources to view the rendered HTML to make sure all your content is showing up.

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.