It's a little elderly, but this article on perl.com may offer some insight: "Building a Large-scale E-commerce Site with Apache and mod_perl".

CGI can run out of steam pretty quickly if you get all your hits at one go, if you have a low peak load, then it can cope quite easily, plus it's easier to work with and debug. While mod_Perl is different from plain CGI, it does force extra code disciplin, which is useful even if you never migrate from plain CGI to mod_Perl.

HTH, and good luck.