Yes, the docs on logwatch are not really in their best shape.
You can delete WARN/CRIT logs from the web GUI. On any log service status page, in the action menu (three horizontal bars) you’ll find the “Open Log” command with some “typewriter” (I guess) icon. On the log page, you then have a “Clear log” command.
To be clear, this is all on the Checkmk server. No need to delete the original logs on the monitored host, since the logwatch plugin remembers its position in the file and won’t re-send lines it has already seen.