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In order to create a Derby database, a connection to the Derby server is created with a url indicating a database name, and the parameter create=true. This is the derby-specific way to create a new database. After creating a database this way, the (now closed) connection that was used is visible in the Runtime tab. There is no reason to show this connection, it will only contribute to confusing the user.
Right click on the connection. The options are "Connect", "Properties", and "Delete". The Properties window allows you to change the Database URL and User. This is very convenient if your database has multiple schemas and users. The state of the connection (Closed and Connected) is reflected in the node. It's a convenience to have the connection status graphically displayed. Users can delete the connection node if they so choose. I would vote against fixing this "defect" if that were possible.
This is how it is supposed to work. The user can right-click the connection and choose connect, which will make a connection to the database and display the database objects (tables, views, etc.) under the connection node.