I've had the same experience as you with Slack and Hipchat. The front end guys with the shiny tools love it, and I live with it.
To the extent you're missing the point... it lets people that might not be able to set it up otherwise have secure messaging across desktop and mobile, and a unified place to have all the features that you mentioned vs getting familiar with nc/scp/ftp, grepping chat logs, etc.
That said, they must have one hell of a demo deck (or secret master plan) to get a $1B+ valuation.