* Companies like Google and Yahoo will encrypt their internal fibre links, and more of the information crossing internet backbones, making passive information gathering more difficult.
* Funding isn't guaranteed. The NSA hasn't really been impacted yet, but it's definitely possible for their budget to be cut in the wake of the ever-increasing revelations. It'll all come down to what the politicians think will get them the most power, and they'll happily go against the NSA if it will further that cause.
* On a slightly longer timescale, a sustained negative public opinion of the NSA will impact their ability to hire the best people.
The impacts on the NSA may not be as significant as you or I might wish, but they're certainly non-zero.