Probably the most used encryption on top of IRC is mircryption [1] and its compatibles [2]. This was popular on EFnet 15 years ago already.

[1] http://www.donationcoder.com/Software/Mouser/mircryption/

[2] There are lots of plugins that add mircryption compatibile encryption to IRC clients on all platforms, e.g. for modern mIRC there's FiSH 10 https://github.com/flakes/mirc_fish_10