I've photographed the CA Mission cemetaries without any problems before. I know at the Chapel of the Chimes in Oakland (only one of the most beautiful buildings in the world!) they ask that your photographs not include any names on the urns.
I'm pretty sure you wouldn't be able to photograph a nude in a mission cemetary... you're bound to run into a priest or sister.
While I've never done nude photography (or photography with a model, unless you consider a rock a model!), I'd definetely agree with the previous poster, to have a person to watch out. People visiting their departed love ones would probably be pretty upset if they saw someone photographing a naked person in the cemetary, especially if it was near their loved-ones' tomb!
You could also try building your own cemetary...