How does the Application Server differenties between regaular J2EE application and J2EE application with Struts framework ? Is it based on following entry in web.xml ?
Yes, it is the entry you mentioned that distinguishes a struts application, along with all associated entries, especially the <servlet-mapping> entry which directs all URIs that end in .do to the action servlet. It is this single servlet directing traffic to the rest of the application that most distinguishes a struts application.
This means that if you want to have your own servlets co-exist in the same application as your struts application, that's certainly possible (although not recommended). Just make sure that the URI you use to call them doesn't end with .do.