Let's ignore all of this for now and simply look at the at the impact of the shutdown on both parties. In the game theory analysis of who won/lost, most are saying Republicans got hurt by the shutdown. (e.g., see link here) If an election was held tomorrow, that might be true. But, once you consider:
1. The next major election is over a year away. Because of this, we have to think about what the mood will be like one year from now.
2. Democrats won't be mad about the shutdown by the next election. They basically "won".
3. Independents won't be mad about the shutdown either as a year will have passed. There will be other pressing concerns. But ...
4. Republicans are mad that they didn't get any concessions, and likely will still be mad about this a year from now. They lost.
Because of this, I think Republicans will do better in November 2014 because of the events that transpired this month.