The main problem solved by CGI.pm is correct evaluation of Query-String or STDINput and the correct output of HTTP Headers. I'd say HTML-generation is a nice feature for small scripts.

As the input parameters and rules for HTTP Headers stay the same under mod_perl (depending on what handler you implement ...), it's still CGI.pm that will do these tasks correctly for you.

As for the HTML stuff: You will agree that in a larger application you'll use templates anyway (i like the Template Toolkit). You only determine the HTML-output in small scripts and for them CGI.pm will save you typing and will produce correct HTML (better "will make it easy to produce correct HTML"). What you do is up to you.