Ok what you said is true but in most cases ducts are in a duct flex format, and knowing that the dust in people's flex duct is just surface dust, any real debris that are in the duct itself will result in very little to no air flow which will keep your unit from performing properly, but if it is true allergy reasons then replacing your duct system is better for overall better air quality, plus if you do pay attention to the warranty on flexible duct is that it only has a 10 year warranty and typically only lasts for 20 years so do your research before having a duct cleaning, and to add one more thing if your duct work is completely metal and you can't see visible insulation then your duct on the inside has insulation inside of it, if you replace that with duct work that is clean metal on the inside and wrapped with insulation on the outside then it will further reduce the air bourne fiberglass and dust.

The short answer is yes, duct cleaning, done right by a reputable company will help with the smell. It is likely though the smell is coming from another source, ie the crawl space. It could also be that another rodent is dead in the duct work. A visual inspection would be in order to check for any breach in the duct system. A duct pressure test would be able to tell you how much air is leaking from the system over all. A hole large enough for an animal to enter would loses a great deal of air, over 300 CFM. It would be worth looking into having this test done and it should cost around $200. Cleaning the air handler and evaporator coil will greatly improve the performance of the air conditioner. Dirt and dust on the evaporator acts as insulation and reduces the amount of cooling done be the coil. Any quality duct cleaning should include cleaning the air handler and coil, and the tech should allow you to watch him perform the work as it is done.
Duct cleaning is a complete scam, I was a “duct cleaning technician” for a whole week before I was fired for not upselling elderly widowed women $2000 extra for “toxic mold remediation” when their ducts were spotless to begin with. The last two days I was employed there I worked as a “helper” alongside a technician thats been with the company 7 years. He scammed every customer on mold and would at times get as much as $2500 extra for treating “toxic mold” in a typical 3 bedroom house in the suburbs. Wait…it gets even better, the “Biocide” the company used was simply a cheap $4.99 per gallon bought at Home Depot air freshener with no anti-microbial properties that was fogged into the HVAC system for 5 minutes, maybe using 1/2 cup of the stuff. In order to provide the customer with evidence of “mold infestation” the technician would be given bogus mold tests that always resulted in “toxic spores present” regardless if you swabbed the actual duct or nothing at all. Not to mention the actual duct cleaning job (typically $400) did basically nothing and the homeowner could’ve done a better job with a shopvac
Duct cleaning has never been shown to actually prevent health problems. Neither do studies conclusively demonstrate that particle (e.g., dust) levels in homes increase because of dirty air ducts or go down after cleaning. This is because much of the dirt that may accumulate inside air ducts adheres to duct surfaces and does not necessarily enter the living space. It is important to keep in mind that dirty air ducts are only one of many possible sources of particles that are present in homes. Pollutants that enter the home both from outdoors and indoor activities such as cooking, cleaning, smoking, or just moving around can cause greater exposure to contaminants than dirty air ducts. Moreover, there is no evidence that a light amount of household dust or other particulate matter in air ducts poses any risk to health.
ISO 16813:2006 is one of the ISO building environment standards.[31] It establishes the general principles of building environment design. It takes into account the need to provide a healthy indoor environment for the occupants as well as the need to protect the environment for future generations and promote collaboration among the various parties involved in building environmental design for sustainability. ISO16813 is applicable to new construction and the retrofit of existing buildings.[32]
I'm very glad that I found another guy to come replace the circuit board and put it away from the water, fix the water leak, and also find and fix another impending failure.  All of that was for much less than HVAC Service wanted to charge for repair or replacement. The other guy did a great repair, so I'm confident it will not break down again, but if it does, I will not call HVAC Service. Don't get suckered by their Yelp Deal.
Duct cleaning has never been shown to actually prevent health problems. Neither do studies conclusively demonstrate that particle (e.g., dust) levels in homes increase because of dirty air ducts. This is because much of the dirt in air ducts adheres to duct surfaces and does not necessarily enter the living space. It is important to keep in mind that dirty air ducts are only one of many possible sources of particles that are present in homes. Pollutants that enter the home both from outdoors and indoor activities such as cooking, cleaning, smoking, or just moving around can cause greater exposure to contaminants than dirty air ducts. Moreover, there is no evidence that a light amount of household dust or other particulate matter in air ducts poses any risk to your health.
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