Imagine if hackers were to somehow to find out where this tool is being hosted and then brute force their way in? Presumably such a tool is heavily secured and off the grid, but if it is somehow accessible from the Internet and an attacker were to find out where, it's only a matter of time now that the cat is out of the bag. Could you imagine hackers having access to troves of metadata and information like that? It's a scary thought.
I'm surprised such a thing took so long to be revealed. If you've got as much data as the NSA has, wouldn't you want a Google like search engine to be able to search through it? It makes so much sense which is why I am surprised some people are surprised about this.