Google reads JS links and methods for a long time. so, if your JS links look like the following HTML-built in JS functions, it wont considered hidden and Google will follow such links:
Code:
1. <a href="javascript:var test=window.open(‘http://domain.com')">my link here</a>
2. <script type="text/javascript">document.write("<a href=http://mylink.com‘>link here</a>");</script>
As it seems, and according to my tests, Google can read JS of known libraries (like jQuery), known built in functions (innerHtml, window.open, document.write etc) and HTML-built in JS functions (like: onclick, onload etc).
Google has real problem to execute JS complex custom-made functions, since the Google crawlers are text-based interpreters that simply parse content / code (hence it's easy for them to find url patterns in your code - even under JS functions), they can't execute (still) complex JS functions since they will have to execute them like a browser - which will be obviously very slow for Google crawlers to do; assuming they have to crawl millions of pages every minute or so.
So, to your question, such links are crawlable, and wont considered hidden text / links