We're not going to be able to back fix v3.2, but version 4.1 is under active development now if you want to try it there. Assuming the 12c JDBC driver will allow you to connect to a 9i database...
SQL Developer 3.2 64 bits does not expand the trees (Tables, Packages,...) when I access a Schema of the Oracle 9i. It returns the error ORA-00942:"table or view does not exist". I debugged the program and saw that it tries to access the view RECYCLEBIN wich not exists in Oracle 9i. It happens only in the SQL Developer 64 bits. For the SQL Developer 32 bits it works.
That suggests that the JDBC jar file you are using (which you did NOT provide any info about) may a newer jar file that doesn't support 9i.
Post the FULL details of your OS name and version the JDK version and the JDBC jar file name and version. The info should include what JDK sql developer is using as well as ALL JDKs on the machine.
Also post a copy of the environment variables that are set that show the PATH and JAVA_HOME settings and the results of a search of the drive that shows ALL JDBC jars files that you have available.