I go back and forth on this. Aptitude seems more reliable in general than cpan, at least in the sense that cpan installations fail more frequently than apt.
Also I assume that cpan packages reflected through apt will be updated with apt-get update, while cpan has no similar update-all mechanism (AFAIK).
One advantage of using cpan is that if you're developing on a Mac and deploying on a Debian distro you can use the same commands on both systems to pull in the packages you need.