Transparency wouldn't prevent the NSA from doing what it does, because they can observe most of the traffic on the Internet, and the phone carries roll over whenever they ask. The argument for secrecy is that people they want to spy on will be able to avoid the spying if they know how it's done, but the only way to avoid it is to resort to sneakernet, and the only countermeasures are the things anyone who doesn't like the NSA/their ISP/J. Random Skiddy looking over their shoulder do regardless of whether they think the NSA cares about what they're up to.
But transparency in the form of Snowden is already potentially going to have an impact on what they do. If transparency leads to scaling-back (which it may or may not), is it beyond the realm of possibility that one day the NSA's ability to collect metadata on domestic calls is removed -- that would certainly hurt them.