As someone said above, a possible cause is that /usr/src was a mount point, maybe with -obind, or even a symlink. Many people do this to handle kernels manually on their own $HOME directory (I do it this way myself).
Another random cause I can think of would be some of the cruft cleaning scripts that there are around and that are not part of Gentoo. On a more paranoid though, it could also be a rootkit, or maybe your box was hacked. But, otherwise, you removed it, maybe without noticing. --depclean would never remove this, even if it was buggy enough to remove all your kernels (which it isn't) it wouldn't remove all the files that do not belong to the package, and there are thousands of these in any kernel tree that's been configured and/or compiled. Hence, the non-empty directories would never be removed either. -- Jesús Guerrero Botella
