What is the purpose of the Assemblies node in Web.Config?
It may or may not be safely removed. The Assemblies node is for configuration-based reference addition. It's used by ASP.NET websites that deploy uncompiled .cs code files to their website, rather than (as sensible people do) compiled assemblies.
If you are deploying code-behind files to your website rather than assemblies, then keep it in. If you are deploying assemblies, remove it.