Does Skype encrypt the IP destination (the IP of the people I talked to) in instant messaging? Now Skype uses the cloud, does my ISP know the IP destination or is my message sent to the cloud?
This answer is adding to @peterh answer
Yes, Skype uses its own networking layer, to deliver messages and voice data, but also Skype provide a lot of information about contacts: there is a SQLite database in local Skype settings. Path for Linux:
$HOME/.Skype/<skypelogin>/main.db. There is a lot of information and probably, it was sent to you through your ISP.
Moreover, there is a some kind of SORM system in most countries; and Skype and most ISP provide an access to the user data in case of investigation of crimes.