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In general, SQL Developer may issue queries that fail on any given database just to check what has been installed. I don't know about the MSysConf query but, for example, if you expand an Oracle 10g XE connection node you will not see a child "Application Express" node. On an 11g EE connection, however, an Application Express node will be present. I imagine the product was just checking for the existence of APEX.
SQL Developer Team