Almost. They still use IRC - but they extend functionality "outside of IRC" with bots. You don't hear this because people make bots with .tell commands that supplement this functionality. The next time a user logs in the bot will /msg them something like "You have 1 message. Use .read list to see a list of unread messages" then they ".read 1" they can then .reply or send their own .tell
Anything IRC "needs" gets supplemented by a bot that takes care of the functionality.