I cant see why the Noctua wouldn't fit the case, it would be more down to your Motherboard I would say.
The fans with the case are ok, pretty quiet on low setting and a little noisy on medium but they are definately not anything special. If noise bothers you and depending on how hot your set up is you can get rid of some noise by blanking off the top hole.
Anyway great case and good luck with your build.