And it's a pain in the neck! It means that some of the participants in the channel are not able to read what's happened while they were away. Some of them get encoding errors. The IRC people do not get the same graphical elements as everybody else. They can't use custom /-commands.
In conclusion, in order to communicate the most effectively, you have to know who's on IRC and think about the differences in user experience for these people versus everybody else.
IRC has weaknesses (namely lack of centralized logging and unspecified text encoding) and fixing these weaknesses means forgoing support for existing IRC clients.
Everyone I've ever worked with who uses IRC has a client or bouncer running somewhere that never disconnects and assumes UTF-8, so neither of these are realistic problems.
A logging program is just another IRC client. Problem solved.