We kinda know what happens if you get sucked into a black hole because of math (spaghettification, what outside observers would see, etc); can the same be said about worm holes? Would you even notice if you passed through one? What would they look like? What would someone watching someone else go through a wormhole look like?
Kinda depends on what that atom becomes once its constituent parts have changed. Perhaps nothing, perhaps it becomes something that explosively cannot exist.
I’m pretty sure a single atom could completely convert to energy, as in perfect E=mc^2 with no losses, and you still wouldn’t notice.
You’d notice if it happened on/near your retina, it was very dark, and you were paying attention. Other than that I don’t think you’re going to notice.