I've often wondered about this.
The cgi-bin directory seems to be a relic of a long ago era.
Before mod_cgi was created and commonly used in Apache, the cgi-bin directory was necessary to execute CGI based scripts.
But now with mod_cgi and the cgi-script handler, any file with a .pl or .cgi (common CGI file extensions, others can be defined) can be executed in any directory (assuming ExecCGI is enabled, which is also common).
You could effectively remove the treatment of the cgi-bin as a ScriptAlias directory and just leave it as a normal directory as long as you have mod_cgi with the cgi-script handler and ExecCGI enabled.
But this also leads to a bigger question. How many people actually still use CGI scripts? Most everything is PHP nowadays.
