I don't know specifically about cgi:irc, but most cgi based irc programs are frowned upon because they connect to the IRC server through the host's internet connection, whereas java irc programs connect using the user's internet connection. The problem with connecting through the host's internet is that A) it puts a huge load on their server and internet connection, B) all users have the same hostmask/IP so they can't be banned effectively using typical IRC commands.
-genius_at_work