> Even if the exposure were for a year, if the amount of light being emitted is less than the hardware can perceive, it wouldn't register
That is not true. It might be noisy, but it would show up.
In point of comparison the human eye can see a single photon.
A single atom can emit a single photon, ergo you can see a single atom.
You won't get any detail out of it obviously, but you'll see it as a dot of light.
That's what's happening here.
> There's a story here about the size of the light being emitted that doesn't seem satisfactorily answered
You are misunderstanding the "size". The size "10,000" is the resolution needed to differentiate between two atoms sitting next to each other.
But in order to see the atom (detect the atom), you just need to be able to capture what it emits. And it emits photons, and it's not that hard to capture and record a single photon.
So you do, and it shows up as a single dot in the image.
If you had two atoms near each other, both emitting photons, you would not be able to distinguish them from each other (i.e. you couldn't say if there were one or two), unless they were farther apart.