Yes, introspection of a WLS domain captures everything in the domain including deployed J2EE application. So yes, the resulting WLS domain after deployment will contain all your applications that you had deployed in the original system before introspection.
All your connections (JDBC, LDAP, JMS) are shown as output endpoints of the resulting WLS appliances after introspection. But none of the applications are visualized in OVAB. Applications are deployed as-is.
PS: Regarding web services in WLS, make sure to refer section B.1.4.4 in OVAB User's Guide: