AS Java Server is not visible from NWDS:
Open DEFAULT.PFL file in /usr/sap/(SID)/SYS/profile and set service/protectedwebmethods to DEFAULT (from SDEFAULT) and then restart the engine.
In case you would face any problem when applying the above solution, then use the workaround:
in NWDS' menu go to Window -> Show View -> Other, and select the Management Console. Right click on SAP Systems, add system, and enter the hostname and instance number. A pop up will ask to enter an adm user and password, enter them both. Then go back to the Preferences, SAP AS Java screen and your system will be there.
See also the note that deals with the popup about the OS user:
#1834579 OS level login dialog appears in SAP MC (Developer Studio) and #2088024 - OS Logon to SAP J2EE Host popup in NWDS
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