I just installed the final release of Web Application Project addon but I think the support for Distributed Application Diagrams is missing.

If I create a new application diagram and I add a ASP.NET Application the designer doesn't have the option to implement it as a Web Application Project and if we implement it manually the application diagram updates itself and adds new Remote Web Service elements.

Is there any plans to support this in the near future?

Yes, support for Distributed Application Diagrams is being investigated for a future releasse.  I can't tell you yet what release but I know it's actively being worked on.

Hope this helps,
Brad.