From experience: the two web-apps are entirely isolated from one another - the libraries for one are not utilised in another - thus to answer your initial question - yes they would be loaded twice.
To answer you second question, whether you should deploy these libraries into Tomcat's shared directory - I would say no, and here's why:
If you deploy a library Jar into the shared location (tomcat/server/lib), then that version of the library becomes the default for all web-applications running under that instance of Tomcat. As you can see from this overview of the tomcat architecture, the class-loader works "down the chain", with an individual web-app's lib folder being the last place it will look before it throws a class-not-found exception. This is not true in Tomcat 6 and Tomcat 7: any classes in the web apps lib and classes folder will be resolved before those in common, and thus, this will not break other apps which deploy all of their jars in the war 2.
The problem therefore of deploying a shared library to that directory is that it breaks the architecture for individual applications being isolated from one-another. Fine in your initial example, but if you want to deploy a third-party application (e.g. if you a running an app that consumes Portlet's to handle specific content), you instantly run in to version dependency issues - your shared version of a library may not be correct for the third-party application, but because the package is already loaded, you'll throw exceptions left right and centre.