Labels that were automatically attached to themes in ArcView 3.x are not associated to any layer when the project is imported into ArcMap. All labels are placed in the active annotation target in ArcMap.
ArcView only has one graphics list per view document, where all imported graphics are placed. The graphic set object, which each theme has when graphics are attached to a theme, could not reliably be used to ensure all graphics were imported just once.
There is no workaround for this issue.