All thing written in
web.config
file are for run time. Meaning used by IIS and your web application. Visual Studio and it's compiler don't used them (except for intellisense). For compile time using of any assembly you must add reference to it using the IDE (Project->Right Click->Add Reference).
See here
http://msdn.microsoft.com/en-us/library/s10awwz0(v=vs.85).aspx[
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This article states that the assembly elements are used during compilation of
ASP.NET that phase done in the IIS just before serving your page as a response...