English isn’t my boss’s native language (although he’s very fluent), so I think he goes out of his way to use colloquialisms like that. He also has a sense of humor. Consequently, he sometimes says some things that sound really weird 1) coming from one’s boss, and 2) coming from a 40-something man with a thick German accent. On the other hand, I’ve heard my labmates say some rather strange things to him, too.
I friended you because I probably should have long ago. (Jonah from Yale House, as may or may not be clear from my journal). I don’t think “what’s up?” is an especially inappropriate thing to say to one’s boss.