The mod:// variant is useful if you a talking about a specific module (bug, detail of use, example, etc.) and the cpan:// variant is useful when exploring solutions to a problem where there may be more than one applicable module.

I've used both variants, but use mod:// much more than cpan://. I think cpan:// is generally over used because it provides a link that is almost always at least one step away from the page of interest to the audience for the link.