2. If air quality is so important and duct cleaniliness is so uncertain, why not adopt doubling filtering; that is, in addition to the existing main furnace filter, add a filter at each air outlet. I understand replacing so many filters would be a burden, but air outlets can be designed for easy filter replacement. The builders and home design engineers should bear responsibility to provide good and low maintenance homes, rather than prioritizing on fancy or costly featuers for homes.
On the other hand, if family members are experiencing unusual or unexplained symptoms or illnesses that you think might be related to your home environment, you should discuss the situation with your doctor. EPA has published the following publications for guidance on identifying possible indoor air quality problems and ways to prevent or fix them.
If there is stuff in the ducts, the fact that it’s laying there and not being blown into the rooms is proof positive that it is hurting no-one. The 5-6 exceptions you cite in this article I’ll buy, but only with the caveat that at least some of those could have been avoided by proper protection (during remodeling for example) – and if asbestos/lead/whatever winds up in your ducts- the remodeling contractor should be the one paying to remove it.

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.

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