I think YC has a lot to learn and will need to invest time before learning how to better pick nonprofits. There are a ton on foundations and competitions that look for nonprofits using technology to innovate the sector. The issue is that very few are measuring impact and asking the question: is this the best way to spend the dollars donated. Nonprofits owe it to their donors to maximize the impact per dollar but this is not something I have ever heard any YC nonprofit talk about yet.
It will be important to pick somebody who has significant experience in the nonprofit sector.
It's great to see that YC will experiment with new models and ideas.