It's important to note that CGI.pm implements a good autoloading mechanism. This means that subroutines are only ever loaded when you use them and that therefore there is very little "dead weight".

Having said that, it's a good idea to take a look at the export sets that CGI.pm provides and start using one that better models the set of subroutine that you use. Personally I always use TT to generate any HTML, so I only every use the CGI.pm subroutines that give access to CGI protocol functionality. For that reason, most of my CGI programs start with:

use CGI ':cgi';
[download]

This means that I can't accidently start using any of the HTML generation functions, thereby breaking the separation of processing and display logic in my program.