You should consider having the air ducts in your home cleaned if:
If any of the conditions identified above exists, it usually suggests one or more underlying causes. Prior to any cleaning, retrofitting, or replacing of your ducts, the cause or causes must be corrected or else the problem will likely recur.
Some research suggests that cleaning heating and cooling system components (e.g., cooling coils, fans and heat exchangers) may improve the efficiency of your system, resulting in a longer operating life, as well as some energy and maintenance cost savings. However, little evidence exists that cleaning only the ducts will improve the efficiency of the system.
You may consider having your air ducts cleaned simply because it seems logical that air ducts will get dirty over time and should be occasionally cleaned. Provided that the cleaning is done properly, no evidence suggests that such cleaning would be detrimental. EPA does not recommend that the air ducts be cleaned routinely, but only as needed. 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.
If you do decide to have your air ducts cleaned, take the same consumer precautions you normally would in assessing the service provider's competence and reliability.
Air duct cleaning service providers may tell you that they need to apply chemical biocide to the inside of your ducts as a means to kill bacteria (germs) and fungi (mold) and prevent future biological growth. They may also propose the application of a "sealant" to prevent dust and dirt particles from being released into the air or to seal air leaks. You should fully understand the pros and cons of permitting the application of chemical biocides or sealants. While the targeted use of chemical biocides and sealants may be appropriate under specific circumstances, research has not demonstrated their effectiveness in duct cleaning or their potential adverse health effects. No chemical biocides are currently registered by EPA for use in internally-insulated air duct systems (see Should chemical biocides be applied to the inside of air ducts?).
Whether or not you decide to have the air ducts in your home cleaned, preventing water and dirt from entering the system is the most effective way to prevent contamination.
Source: Environmental Protection Agency