I think what your DBA did was nice, but not a good idea.
Overloading the data dictionary object names seems questionable, at best.
Our friendly DBAs gave us a view over DBA_SOURCE so that we could see the code in the package bodies and so the schema has local synonyms for DBA_SOURCE and DBA_OBJECTS.
IMO, it's always a bad idea to replace well known public synonym names with private synonyms of the same name. These type of things are bound to happen with this approach. This is not SQL Developer's fault.
When I need to do something similar, I remove the "A" from the name. So it becomes DB_OBJECTS. This way, I don't have any potential for name collisions, but the object name is still just as meaningful. Maybe the DBA can do something similar for you.
As i said, I've got no issue if SQL Developer consistently wants to explicitly refer to SYS.DBA_* objects.It is the inconsistent referencing that is results in the error.
We could rename the DBA_**** synonyms but so far it is only SQL Developer that has an issue, and some of the team use TOAD which works better with the synonyms.
As an aside, we also have synonyms for some GV$/V$ views too, limiting to a subset of schemas. Oracle built-ins such as DBMS_SQL.DISPLAY_CURSOR need those exact names to function so we can't use alternatives there.
[Personally, I don't care if it gets fixed. I've put up with it for several months, and only raised it because another team member asked me about the problem. The attitude in these forums suck, and I avoid coming here whenever possible. In future I won't bother raising issues.]
There's not really a bug here, so there's nothing to fix. If you want to report a bug, please open an SR with MOS.