The marker should indeed disappear if the pick up point is turned off, or change colour and/or use a different marker.
Increased priority since this may have given us false reports in the past, the AI will fly to a disabled pick up point but not dock to it if it is disabled. If you don't know that you can disable it, or because in a disabled state the texture only rotates, it's easy to misunderstand this as a bug when it refuses to dock.