The following help article treats this case: http://www.telerik.com/help/aspnet-ajax/introduction-add-to-global-assembly-cache.html
Similar reports are abundant in the net and there are some workarounds, for example this tool
for WebApplication projects.
Why Visual Studio wouldn't find the references is a question perhaps only Microsoft could answer. Since the assembly is there and is registered they should find it. From what I can gather from similar complaints in the net - indeed registry manipulation may be required so that third party assemblies are shown in the VS list. After some research in the net here is a list of resources that can be helpful for you in this regard:
Nevertheless, I can suggest two ways to work around that Visual Studio limitation:
1) that you add the reference by browsing to the dll (the Browse tab, go to %windir%\Microsoft.NET\assembly\GAC_MSIL\Telerik.Web.UI\v4.0_2012.3.1016.40__121fae78165ba3d4 or whatever the folder gacutil created for you and just add that). It should reference the GAC deployed assembly regardless of the fact that VS cannot find it in the .NET list.
2) add the reference directly in the web.config, e.g.;
"Telerik.Web.UI, Version=2012.3.1016.40, Culture=neutral, PublicKeyToken=121FAE78165BA3D4"
where the version will vary with time, of course. The gacutil tool can be useful with its l-slash to get the exact versions installed in the GAC.
the Telerik team
If you want to get updates on new releases, tips and tricks and sneak peeks at our product labs directly from the developers working on the RadControls for ASP.NET AJAX, subscribe to their blog feed