I was standing around in Nipton, ate some Maize and then some spooky music played and the Vault Boy notification popped up with ... as the info and his eyes were spiraled. Was it some kind of random encounter? I explored the area but found nothing.

bad maize i'd say..

I had the same thing when I killed the robot prototype while exploring Nipton after the Legion left. What does it mean?

Ah I can answer this! That means that you have encountered one of the Wacky Wasteland events, that icon appears when you are near a Wacky Wasteland event you know what I mean? I haven't a clue why you have not found this... It is usually right in front of you when you hear that music. But yes that is why.

Did you take the Wild Wasteland Trait at the beginning of the game?