"... what performance penalty I'm paying for including documentation in my Perl CGI scripts ..."

Effectively none. Perl compiles your code to an internal form at run time at which point any comments and pod become irrelevant. There is no "Perl compiler". For websites with modest traffic you can pretty much ignore any startup overhead that is incurred by perl getting going. If you have a high traffic site it may be worth investigating mod_perl and its ilk.