There are 2 sides for your question:
First: whether it's a good idea for a Japanese company to start business in KSA or not, and this is where I shouldn't give you any advice since I'm not an expert :)
Second: whether it's good for you personally to move to KSA and work there, and the possibility that it might not be safe for you. At least I can answer this one because I have part of my family there and they're living and working in 4 different cities in Saudia; I can tell you it's very safe because life is so normal there :)
I know that we are surrounded by ISIS, even in my country in Jordan, but honestly it's safe to live in both (Jordan or KSA), yet I get it when you fear coming to our part of the world because of what you hear on the news. ISIS are in Syria and Iraq and living in both is not safe at all.
I hope I answered you in a way that helps you to take a logical decision, good luck :)
Believe me, when it comes to ISIS, it's not about you being experienced in living in Islamic countries or not, because they don't care! They brutally kill who ever they caught, so I don't consider them human beings or even Muslims!