EPA does not recommend that air ducts be cleaned except on an as-needed basis because of the continuing uncertainty about the benefits of duct cleaning under most circumstances. EPA does, however, recommend that if you have a fuel burning furnace, stove, or fireplace, they be inspected for proper functioning and serviced before each heating season to protect against carbon monoxide poisoning. Some research also suggests that cleaning dirty cooling coils, fans and heat exchangers can improve the efficiency of heating and cooling systems. However, little evidence exists to indicate that simply cleaning the duct system will increase your system's efficiency.
You should be aware that although a substance may look like mold, a positive determination of whether it is mold or not can be made only by an expert and may require laboratory analysis for final confirmation. For about $50, some microbiology laboratories can tell you whether a sample sent to them on a clear strip of sticky household tape is mold or simply a substance that resembles it.