Is there a stand-alone chat client for Battle.net?
The recently released Battle.net Desktop App now includes the ability to chat with your friends if they are logged on to that same app, or any of WoW, SCII, D3, Hearthstone, Heroes of the Storm or Overwatch.
I shortcut all Games in Steam, even WoW and Starcraft 2. Starting the Games from the Steam lib works without probs. That way they benefit from the steam chat function. As long as your pals do the same you have no problem chatting across games. Tell your pals, tell everyone. Make it the popular thing ;)
No. Blizzard is slowly moving in this direction, with the recent announcement that players will be able to access their World of Warcraft guilds chat, as well as direct messaging with guild members via the Armory and it's Mobile apps for iPhone and Android.
As to when this feature is expanded to Battle.net as a whole? Nothings been announced, but I doubt you could go wrong with Blizzards characteristic 'Soon™'.