Point defects in large area junctions appear as small leakages,
noise sources, locally-reduced breakdown, that kind
of thing. But when you get down to leading-edge geometries
the "point" can be on the order of the device and not so
small a matter anymore. You can see even the statistics
of dopant distribution (which you would think of as uniform)
in MOSFET VT nowadays.
If you etch a hole you are introducing effectively a metal-insulator
interface across its length (not to mention contamination
and surface nonuniformity effects) and I would not offer a
general theory, because it's going to be down to the(literally)
dirty details.