While this posting doesn't specifically discuss solution design, it does discuss the performance implications of single assembly vs. multiple assemblies.
http://blogs.msdn.com/junfeng/archive/2004/02/23/78139.aspx
Junfeng Zhang works on the Fusion team and has some good insights.
The bottom line is one assembly is better from a performance perspective than multiple. However there are other benefits of multiple assemblies such as increased modularity and extensibility to name a few.
-dan