If you had a way to find all the project directories of these referenced projects (containing the nupkgs) inside the NCrunch workspaces, would you be able to use this instead of hard-coding build references to these projects?
NCrunch has a concept called 'Implicit project references' that is designed to allow you to do this. The caveat here is that implicit project references are only available at run-time, not build-time.
Check it out -
http://www.ncrunch.net/documentation/V3/reference_project-configuration_implicit-project-dependencies.
The idea would be that you'd set implicit project references from your test project to the projects containing the nupkgs, then you could enumerate these using NCrunch.Framework.NCrunchEnvironment.GetImplicitlyReferencedAssemblyLocations() and working back from the DLL to the project directory. Such an approach would only work under NCrunch, so you'd need to have two different versions of your test if you want it to be run outside NCrunch.
Note that if you already have project references pointing at the nupkg projects, then you won't need to specify an implicit project reference .. you'd just use NCrunch.Framework.GetAllAssemblyLocations() instead.