In addition, the service provider may propose applying chemical biocides, designed to kill microbiological contaminants, to the inside of the duct work and to other system components. Some service providers may also suggest applying chemical treatments (sealants or other encapsulants) to encapsulate or cover the inside surfaces of the air ducts and equipment housings because they believe it will control mold growth or prevent the release of dirt particles or fibers from ducts. These practices have yet to be fully researched and you should be fully informed before deciding to permit the use of biocides or chemical treatments in your air ducts. They should only be applied, if at all, after the system has been properly cleaned of all visible dust or debris.

The Environmental Protection Agency says that “duct cleaning services typically – but not always – range in cost from $450 to $1000 per heating and cooling system, depending on the services offered, the size of the system to be cleaned, system accessibility, climactic region, and level of contamination” and type of duct material. Consumers should beware of air duct cleaning companies that making sweeping claims about the health benefits of duct cleaning – such claims are unsubstantiated. Consumers should also beware of “blow-and-go” air duct cleaning companies. These companies often charge a nominal fee and do a poor job of cleaning the heating and cooling system. These companies may also persuade the consumer into unneeded services with and/or without their permission. (If you have knowledge of a practicing “blow-and-go” air duct cleaner, contact your local Better Business Bureau to report the company, and your local, federal, and state elected officials to demand legislation.)
The fact is if they are dirty why not clean them. As for the Dr’s comment about if it is not disrupted it is fine. As a pet owner sometimes un disrupted pet hair will sit in the corner of a room or under a counter un disrupted but I still clean it when I notice it. Just because you cant see it doesn’t mean you should leave it there to collect more and more. The people that don’t want there air ducts clean either simply cant afford it but would like it done. OR! the crowd that are to cheap.. You should Clean all portions of your house.
There are many interesting comments from several informed individuals. The question that has not been answered is how do duct systems get dusty and dirty? As a RESNET Home Energy Rater, I perform pressure tests on homes and duct systems, and the one common thread is . . . most air delivery sytems have large amounts of air leakage. The solution is to seal the duct system, and pay particular attention to the return duct system and ductwork near the air handler (the 'blower'). As others have said, a captive (sealed) duct system with proper filter maintenance should be more then adequate for most occupants. For those who have allergy, asthma, or other breathing problems, a filter with a higher MERV rating (number should be listed on the package) or a HEPA filter are good choices. These filters will capture smaller particulates and should improve the indoor air quality. Again, make certain that the entire duct system is sealed, preferably with mastic, second choice UL-181 foil tape - never use cloth duct (also known as duck) tape.
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.