I don't see the advantage for google to hide the searches of those that are logged in. I would expect it to be an opt-out system. In fact, I doubt there will be a major change from what we have now except that it sounds Google is doing what they should have done in the first place.
My more technically inclined friends always told me to sign out of Gmail when searching on Google because all the information gets tied to you so much more closely if you're logged in to your account, but if they make the search info of logged in users anonymous now, that's a perfectly logical and happily welcomed move.
This might even make SEO easier as people like me will feel comfortable being logged in while searching if my search is treated with the same respect to privacy as any other!
Google loves SEO, it's what develops their main product. I don't see this being a big burden at all; they have so much more to lose than gain from this and it would be the first case in recent memory where an information company actually gives MORE privacy.....and that doesn't seem likely.