Yes, Google Analytics uses js. If you want to count real people, it can be argued that js tracking is actually a better way to go than site logs, even though some visitors will have js off.
Is there anything to suggest that the type of traffic you've been getting recently... ie, in say research vs commercial... is different enough to cause the changes you're seeing? With regard to traffic from Google, or from sites that found you via Google, this thread might provide some food for thought...
Google & Traffic Shaping - a hidden method to the quality madness?
Also, in the period you're looking at, keep in mind that this was an election year, and that the economic situation is uncertain at best.