Are there unobservable, undiscovered atoms? Is it possible that there is a network of atomic activity that our current scientific instrumentation cannot detect? 
In other words, could it be possible that there are unobservable, undiscovered atoms that are perhaps smaller than what we consider currently atomic?
 A: At the Large Hadron Collider we have studied matter down to a length scale of about $10^{-19}$ metres, which is about a billion times smaller than an atom. All the results so far confirm our existing theories. So it seems very unlikely that an undiscovered class of small atoms exists.
The size of an atom depends on well understood physical principles. At the risk of oversimplifying, if you try to compress electrons into a small space their energy goes up due to the uncertainty principle. The sizes of the atoms we see around us are a trade-off. Electrons want to get close to the positively changed nucleus, but as they shrink towards the nucleus their energy goes up. Atoms end up at a size where the two effects balance out.
It is actually possible to make smaller atoms by replacing the electrons with muons. The resulting muonic atoms are about 200 times smaller than the same atoms made with electrons. However muons are unstable and decay after a few microseconds, so sadly we never see these muonic atoms in nature.
A: Oh yes, certainly. Of course there is, by your definition, no way to determine this, even in principle. Since these "ghost atoms" are unobservable, they emit no radiation that we can sense. Unlike dark matter, whose existence we have deduced from gravitational effects, they do not affect us gravitationally. They do not collide with regular atoms, and they do not affect either electrical or magnetic fields. Because they do not affect light, they do not possess color (not white, not black, not ANY aspect of color). Oh yes, and since they cannot be compared against any material object, they do not possess size at all, and so asking if they are larger or smaller than "what we consider currently atomic" is meaningless.
In other words, they might as well, from our viewpoint, not exist. And from their viewpoint we do not exist. So what does it mean to ask "Is it possible that there is..."? 
