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 ...

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.

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 ...

Bucko described a test they did showing significant delays by Googlebot following links in JavaScript-reliant pages compared to links in plain-text HTML.