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.
Rick Strahl's Web log has short but concisely explaining article on the subject.