I can't comment on the structure without some more information - are those directories named after CPAN modules dependent on those modules? That's not how I would do it myself, but as long as you like it I suppose it's fine. Or maybe they're vendor distributions of the modules, versus your local modifications of those modules. If that's true, then it's a bad idea, for several reasons.

Anyway, I prefer one big repository for all projects, with separate sub-structures for each project. It makes backing up the repository atomically much easier, but you can run into space issues. As always, TIMTOWDI. :)