I replaced all the ducts but the trunks in my 1969 home when I replaced the horizontal furnace under the house with a gas pack. I got advice from a friend who was an HVAC contractor. I was surprised to find the trunks and other ducts very clean. I replaced the individual runs with flex primarily for the insulation. I wrapped the trunks with insulation also.

Yes everyone should get all their ductwork cleaned, because it does help, incame down with major allergies and had serval operations on my sinues because of this problem of air quality and dust, plus i almost died from one of the operations, i was suffering so much. Yes you can seal your duct system by buyind duct seal t instead of tape to tape all the corners of the vent system, tape wears out and gets brittle, the sealant you can buy at home depot, and you just brush it all over the connections of your ductwork, it comes in a container and it is like a thick paste and dries making a good seal for your ductwork.
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.
Heating, ventilation, and air conditioning (HVAC[1]) is the technology of indoor and vehicular environmental comfort. Its goal is to provide thermal comfort and acceptable indoor air quality. HVAC system design is a subdiscipline of mechanical engineering, based on the principles of thermodynamics, fluid mechanics and heat transfer. "Refrigeration" is sometimes added to the field's abbreviation, as HVAC&R or HVACR or "ventilation" is dropped, as in HACR (as in the designation of HACR-rated circuit breakers).

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I just had my blower module replaced because my AC coil was frozen over. The underside of my coils had a thick mat of dust because I had never had it cleaned. I cleaned it myself by using a soft brush attachement on a shop vac. The inside of the blower appears to have a white/green growth, and I am sure the ductwork of my 30 year old house can’t be in good condition.
Pro Tips: Before you buy one of the learning thermostats available, you should beware of their shortcomings. First, many require a c-wire to work properly. A common problem is that the old thermostat might not use a c-wire, and this makes it confusing when swapping wires to the new thermostat. Secondly, if you change your thermostat setting often, you might become frustrated with a nest thermostat or other learning thermostat. It will be constantly trying to learn patterns in your random setting changes, and will therefore change your home’s temperature when you don’t want it to. If you have a fairly consistent schedule or don’t mind overriding the unit either manually or via the app on your way home or when leaving, then you won’t experience this issue.
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.
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