I hate to spoil all of your conspiracy theories, but I think your son hasn't done anything wrong. He actually seems like a pretty normal computer geek.
Raspberry Pi is actually a type of cheap miniature computer. Think of a laptop about the size of a phone. Of course, a Raspberry Pi has less capabilities compared to a laptop, but it's useful because you can reprogram it to do many different things, like control robots. "Hacking" it means you reprogram or rebuild it to do new things.
Lubuntu is a type of "operating system," like Windows or Linux. It's the interface between binary (what computers use to store and process data) and plain English (what users, like me and you, use).
Skype is a program that allows you to make telephone calls over the internet. For example, if you "Skype" someone, a live video feed from their camera will appear on your screen, and you will be able to talk to them just like you would in real life.
This is all perfectly legal and well-known computer software. Furthermore, instantly assuming that a Middle-Eastern-looking person is a terrorist is racist and very judgemental. There are many smart, talented, and capable Middle Eastern people in excellent schools such as MIT, Harvard, and Cornell.
Honestly, for all you know, your son is a genius at computer repair or electrical engineering, and was talking with a professor at an Ivy-League school about electronics projects. I think you're going overboard with your reaction (was there any evidence he was working with ISIS? How on earth would he "hack the world", anyway?)
Just calm down, and talk to him about it. Let him explain what he's doing, and maybe you'll even pick up some computer jargon, so you'll be less worried the next time he Skypes with someone. He's 17. Give him some freedom- he's not going to live with you forever, you know.