The encrypted searches will only occur on Google.com and not on affilate search applications. In order for the encryption to occur by default, a user must be logged-in. Google lead engineer, Matt Cutts, believes that this default behavior will only take place for a single digit percentage of searches. If he is correct, there will still be a large amount of web referrer traffic data to "play" with, but certainly website SEO agencies and marketing practitioners won't be happy at this loss of vital performance data.
Some companies, external to Google, have argued with Matt Cutt's estimate of a single digit percentage of affected searches. Nevertheless, the data protection is good for users, as concerns over data protection only grow in an increasingly web-centric world. Google seems to be learning from the mistakes and lack of concern that Facebook bestows on it's users and community, which some believe will be Facebook's undoing.