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Yeah, but we don't know from the class name itself whether the class is in a file with the same name or not. So the best we can do is always print NameOfClass.java:1, even when NameOfClass.java doesn't even exist.
Yes, clicking through packages is definitely a pain. I'm using IDEA and always open files through CTRL-N and paste the name of the class.
This should really be handled by the IDE itself. Instead of only creating a link when it sees Something.java:123, it should also create a link every time it sees a fully qualified class name in the output window (similar to how IDEA does this in XML files).