If yes, why? If they are sometimes good, is there an exhaustive list of what would qualify?
They are ok if they represent features at different locations in 3D space. That is, if latitude and longitude are identical, but elevation is different. Such nodes aren’t true duplicates, they only appear to be because elevation isn’t a first-class citizen in the OSM data model. (Instead, elevation might be indicated by tags, e.g. different level=*
tags in Simple Indoor Tagging.)
There have been historical US imports that brought in different features with identical coordinates: for example - roads and boundaries. In general it would be wrong to automatically combine duplicate nodes with a bot, as that makes the later manual update operations much more difficult. In some cases it will damage the road topology, such as combining a bridge node with the road below it. (people didn’t always set the level tag when creating bridges in the old days)