Annotations created in ArcGIS 9.x served by ArcIMS 9.x ArcMap service, affects the total number of layers in the layer list versus actual number of layers in the layerlist of HTML viewer.
One ArcGIS 4.x annotation layer is interpreted as one layer by ArcIMS 4.x and ArcIMS 9.x; on the other hand, one ArcGIS 9.x annotation is interpreted as two layers by ArcIMS 4.x and ArcIMS 9.x.
If you create an annotation layer at 9.x – a group of two layers is created. If this annotation is loaded into ArcMap, the annotation layer is now group of two layers.
The ArcIMS Server returns this layer as two separate layers. By default HTML viewer is designed to show all the layers in the table of contents, so one annotation layer will end up being two layers in the table of contents of an out of the box HTML viewer.