I'm a little surprised that Daniel notes "around 50% of Perl and Python source files had no license;" This is the case surely on CPAN, missing licenses are a well known problem on CPAN since most people take it for granted that their module will be "the same as Perl" when it comes to a license.
However, I've done some packaging of CPAN modules for Debian and I know many of the people who have been doing this in the pkg-perl team in Debian for a number of years. I note that there are very strict rules regarding licenses in Debian and I've seen that it is exceedingly rare that a CPAN module gets uploaded into pkg-perl staging area without a license and nearly impossible for a CPAN module to get past the Debian ftp-masters without a license. Often the license is in the top level directory and documented in the debian/copyright file, seldom do perl module maintainers add a header to every file even if they're using the GPL.
Because of this I would have thought that perl modules would have been better represented by their module license as opposed to the per file mechanism and I think that would have led to 100% license coverage, at least in Debian.