Moisture can enter the duct system through leaks or if the system has been improperly installed or serviced. Research suggests that condensation (which occurs when a surface temperature is lower than the dew point temperature of the surrounding air) on or near cooling coils of air conditioning units is a major factor in moisture contamination of the system. The presence of condensation or high relative humidity is an important indicator of the potential for mold growth on any type of duct. Controlling moisture can often be difficult, but here are some steps you can take:
Duct cleaning is a band aid, like washing you hands is. Under your description, why wash your hands more than once? If it gets cleaned once, it shouldn't get dirty again. Well that is, unless they touch something dirty. Keeping your hands completely clean is virtually impossible. Same as keeping dust out of your home. You clean your ducts and over a 3-5 year span they get dirty again. Also, duct cleaners are not licensed but should be certified by NADCA(National Air Duct Cleaning Association).
All these pro duct cleaners answer with "it's common sense, everything operates better when cleaner" etc. But your explanation is correct. Especially so with flex tube ducting where dust gets "stuck" between the lowest valleys (between wire coil supports) where air flow is drastically reduced -- which is more than 50 pct of the entire interior surface area of the flex ducting. That sounds like a bad thing but also has a good effect of trapping dust from escaping.
A small number of products are currently registered by EPA specifically for use on the inside of bare sheet metal air ducts. A number of products are also registered for use as sanitizers on hard surfaces, which could include the interior of bare sheet metal ducts. While many such products may be used legally inside of unlined ducts if all label directions are followed, some of the directions on the label may be inappropriate for use in ducts. For example, if the directions indicate "rinse with water", the added moisture could stimulate mold growth.
Air duct cleaning service providers may tell you that they need to apply a chemical biocide to the inside of your ducts to kill bacteria (germs) and fungi (mold), and prevent future biological growth. Some duct cleaning service providers may propose to introduce ozone to kill biological contaminants. Ozone is a highly reactive gas that is regulated in the outside air as a lung irritant. However, there remains considerable controversy over the necessity and wisdom of introducing chemical biocides or ozone into the duct work.
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 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?).