The question is interesting but I don’t believe there is a data problem here.

Deelgemeenten are tagged exactly once as an outline, and do not overlap.
But each object also has a centre node with place=*.

I suppose the user is referring to the search box on the osm.org website, i.e. Nominatim.  Indeed, Nominatim always returns the two objects when given a name.  They are nested (the node is the "centre" point of the area), it is not a duplicate.

(Even Belgium has a "duplicate" in that case, see https://www.openstreetmap.org/node/1684793666)

Onkerzele is treated exactly as all other deelgemeenten.  Same behaviour for Nieuwenhove, Schendelbeke…  One relation with the full perimeter and one centre node.