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I've been to pages with badly written javascript that spikes your processor pretty bad. All this would be extra processing done by the spider and maybe the search engines don't want to get bogged down with extra processing.
More [google.com]
It's notable to mention that SE's may read the content in Javascript but won't execute it.
So it's likely if you have the script inline, at the head of a document or writing inline in the page with document.write() containing links, it will probably pick it up.
But if you use external js, it may not. I've never fully chased this one, if you want your links to be followed, use plain ol' links and apply JS to the objects containing them to show/hide, whatever.