What is the origin of the "Hidden" event in Fairy Tail?
The origin is literally impossible to trace. At best, we'll see who implemented this idea first but it could have been thought of a long time ago or done in many things that we don't have knowledge of. Hiro Mashima (the manga-ka) might be able to say where he got this or why he decided on this but its not exactly a rare idea to do this. Its pretty much a simple twist on a "zero sum" kind of game. I'm almost certain that Assassin's Creed was not the first to do this.

Come to think of it, in earlier chapters of Fairy Tail, Mashima used to scribble "Mashima's ramblings" in the gaps or sides of the page. From these "ramblings", we know Hiro Mashima does play video games (and at the very least, owns a PS3). So even if Assasin's Creed multiplayer was not the first to implement this system, there is some offchance that Mashima got the idea from playing that game.