You are of course correct, I just checked a controller and cannot find WebSphere under the Web Application Servers part. WebSphere MQ seems available though. Perhaps one needs to enable the app server monitors in some way? We use SiteScope for most monitoring so I seldom find any use for the built-in options in the Controller.
Anyhow, I believe you are entitled to a 500 point SiteScope license if you have purchased a LoadRunner license. Call your HP contact/license person and ask about it.