It shouldn't affect Google Analytics and other JavaScript based analytics, but from the article,

* If this becomes popular it has the potential to skew logs and stats. Consider what happens when a bunch of prefetch requests are made to one of your pages, but the user never actually visits the page. The server (or stats package) doesn’t know the difference.

To clear this up, Firefox sends along an HTTP header, X-moz: prefetch, but you need some logic on the server side to detect it.