I have to disagree with anyone that discounts the enormous value of the data being collected. If you can't see it, then you just don't understand. I have a 20+ year background in retail at the corporate level. I've worked with merchandising, marketing, purchasing, and data analysts in that time. There isn't a company in the world that wouldn't love to be able to track people through an environment like WDW.
If you are disgruntled with seeing the same merchandise in multiple shops and it turns out that you are not alone, then I guarantee you Disney will see this in the data and react accordingly. The downside is that if they believe that spreading best-sellers around the park regardless of theme is working, then you'll continue to see status quo.
Keep this in mind: tracking inventory movement is industry standard. Most retailers can see items sell on a daily basis, if not in real time. They also study patterns and make merchandising and marketing decisions based on that data. But imagine being able to tell not only whether or not someone bought an item on their visit to a particular shop, but their age, the number of people in the party, where they've just been, how long they stayed, and where they are going. The possibilities are endless, and I think, ultimately, it's going to help them make better decisions that maximize profits. If keeping the theme of a particular land or park is as important as you believe it to be, then it will change.
If anything, I expect them to fine tune the capabilities of the system to increase precision and capture more data points. Like it or not, do not discount the power of what they have created here.