Hi, thanks for posting!
At present, no formal testing has been performed with NCrunch on .nuproj projects. No specialised code has been written to handle them, and no analysis has been done. To be honest, my own experience with these project types is pretty close to zero.
So I think it's safe to say that this is an unsupported project type. Any success you have in using NCrunch with it is entirely accidental and due to the abstractions involved. We really can't warrant that it will work at all.
If you'd like to see support extended to this area you're most welcome to
vote for it on uservoice.
Meanwhile, I would suggest turning off these projects under NCrunch using the 'Ignore this project completely' setting. If they contain code that you need to target using your tests, I'd suggest moving this code out to a separate project (a non .nuproj one) and accessing it through a project reference. In this way, you can target the code using normal test projects and still use the .nuproj for generating your packages for deployment.