Your question is a little esoteric, I have to warn you. It is very rare in chemistry to think about possible reactions of a single molecule in a "perfect" vacuum, because it is very rarely that we conduct experiments under those conditions. We prefer to experiment with things in bulk, and speak of probabilities in bulk.
I also don't see what advantage your thought experiment provides: Why does it have to be just one? If just one, among a group of trillions of other molecules in a droplet of water decomposes ... isn't that the same? Why does it have to be in a vacuum? If it happens in a droplet, it is no more or less easy to see than isolated alone in a vacuum. With the added difficulty of isolating it alone added to the difficulty of detecting its decomposition alone.
Considering a beaker of water, on a lab bench, located somewhere on Earth: Will some of the molecules decompose, so you mean, break into hydrogen and oxygen? Not without significant energy input -- electric current, for example will decompose a large bulk of it, and we'll be able to see the hydrogen and oxygen gasses. That's much simpler to understand. And yes, theoretically, we assume that a single molecule, subjected to enough energy, will break the bonds holding it together, and stop being water, and start being a pair of hydrogen ions and an oxygen ion. (Because you've given it no other molecule to make a full oxygen molecule.)