If they are simple holes with cylinders and perpendicular planar faces, it’s not all that bad with subobject editing. But something just slightly more complex than that - such as the stepped hole in the example - become problematic quickly - for one main reason. To “remove” the stepped part by bringing the larger hole diameter down to the smaller hole diameter requires that the planar surface between the two be completely removed. This is what Rhino does not know how to do.
This affects variety of subobject editing operations, not just round holes. Anytime one tries to reduce a surface inside a polysurface to 0 in one direction via subobject editing it will fail - even something simple as moving one edge of a box to a parallel edge to create a wedge shape, as a remnant of the surface that should just disappear gets “stuck” in the polysurface and makes the whole object invalid.
Until cases like this can be solved, subobject editing of things like holes and such will be pretty limited. In the end it’s easier to eliminate the hole completely and re-make it from scratch.