The files that show ship silhouettes in the map are the _shp.tga ones in all individual ship folders in Silent HunterIII/Data/Sea, for example "NCO_Flower_shp" displays the Flower silhouette from above in the map. Some mods like the venerable Real U-Boot made those tga fully transparent so that even with "Map Updates" turned on, you could not see in the map where the enemy ship is. However, you can still get the rest of items not blanked out, like in this case, the sonar contact lines (Which are "contline.tga" in Silent HunterIII/Data/Menu/Gui).
So, if you want to delete ship silhouettes but keep the sonar lines, create new, empty _shp tgas for all ships and overwrite the existing ones.
