According to the NDepend support response, which I'm posting here for reference:
NDepend project takes a list of assembly name (without file extension) and a list of directories. It then resolves assemblies in these directory by name, and if several assemblies with the same name are found, you get the error.
What you can do is go to : NDepend > Project Properties > Code to Analyze > Folders and erase the folders of the branch(es) you want to discard.
This did seem to resolve the issue for me.