What is difference between web.config assemblies element and project file Reference element
In the web.config section:
The assemblies element defines a collection of assembly names that are used during compilation of an ASP.NET application.
Web site projects usually use the assemblies element as there is no project file storing location of references that the web site uses. The project references would not apply to a web site, as it has no proper project file to store these in, so must store all referenced assemblies in the web.config. There is some interesting, although not directly related, discussion here.
Web application projects may make use of both the assemblies element and project references.
Having a reference in the assemblies element also means you won't have to add the @register at the top of any .aspx pages that use that namespace. More discussion on that here.