Yeah so it seems we finally got bug #155590 fixed. Should make java-config-2 split out an error message if package.env is malformatted. This is better for little scripts than just ignoring extra quotes inside the CLASSPATH variable.
*** Bug 165126 has been marked as a duplicate of this bug. ***
This is better suited for java-check-environment that now checks for commas in there but not for quotes that bug 155590 was originally about.
I don't think this has been an issue for sometime and seems it was due to 1 package and/or a bug in an eclass per linked closed bug. I think this might be able to be closed now as invalid. Not sure another package has had such issues. Quotes can be filtered out from depend, but not sure anything is adding extra quotes there or any since 07.