I created an Outlook 2010 addin project, then I created a Visual Studio 2010 setup project. I right-click on Setup project->Add->Project Output
On the popup dialog that appears, I select my addin project from the dropdown, choose Primary output from the listbox, and from the Configuration dropdown, I initially chose something other than '(Active)'. When I did that, the Detected Dependencies for the setup project don't show up--just the Microsoft .NET Framework shows up. Only when I remove it, start over, and chose '(Active)' from the Configuration dropdown do the complete list of dependencies appear.
I have also reproduced this using Microsoft's own sample Excel addin from the following location:
http://code.msdn.microsoft.com/VSTO2010MSI
For that sample code, I opened the FX40\AddIn Deployment solution. Then I immediately deleted their setup project and created my own. IMPORTANT!!- to reproduce the odd behavior, you must first add any Primary output other than (Active). If you first add (Active), delete the primary output, then try adding something other than (Active), I believe the dependencies WILL show.