Previously... After using setFormalCharge instead of setCharge, some of the null atom types disappeared. Specifically, the quaternary (SP3?) nitrogens, that have to have a +1 formal charge.
What is left? Mostly FeS clusters, and other metals. Turns out that the height-1 signature is clearer for 'clustering' the atoms into types. This is because a signature of this height records only the immediate neighbours of the atom.
One fairly frequent example is "[Co]([N][N][N][N])", but fortunately there is a patch for this based on a bug report. The atom is found in cobalamine and other cobalt-haemes.
Still, there are quite a few 'odd' ligands - either due to unusual elements, like Iridium; or unusual coordinations, like this iron with 6 oxygen neighbours. Hmmm, PDBeChem's image (at the bottom of the page) doesn't show all six bonds. It's clearer in Jmol from PDBSum, where the C3 symmetry of the iron ligands makes it seem (to me) that it is 6-coordinate.
Wow, that's a lot of links.