I own an HVAC company. Dirt in your ducts stays there and hurts no one. It is like dirt on the ground outside. This industry was infiltrated by a bunch of money grubbing low lifes years ago. As a credible company, we do not clean air ducts. Some who were credible probably signed on not knowing what else to do or to try to make a buck another way. These companies, because they also do HVAC work not only rip off private homeowners, they are ripping off legitimate HVAC company's customers and the integrity of what can and should as a rule be a great service industry. Some probably have gotten into this to simply offer what competitors who were ripping off their customers were offering. Anyone cleaning ducts is in my opinion raising a big red flag that they cannot and should not be trusted. Political pressure from NADCA, advertising dollars, manufacturers and marketers of duct cleaning equipment, and intense competition for the customers is the only reason the government and adverstising companies have not run them out of business and that this cancer perpetuates itself.
If the system is sealed air-tight and a really good filtering system is in place then you should NEVER have to clean your ductwork. Most dust people see in their homes (on beds furniture etc....) is broken down insulation that is being blown into the home from the attic (venturi effect) where the duct bucket (box etc...) is not sealed at the sheetrock ceiling. On the return side, ANY leaks in the ductwork will pull hot attic air and dust into the system, clogging up everything.
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.
He proceeded to clean each heat register by removing the grille and blasting it with an air pressure hose toward the duct opening thinking that the dust would magically be sucked inside. In one room this caused a ceiling smoke detector to go off because the excess dust fooled it into thinking there was smoke. I put my hand in front of a register he wasn’t working on and could hardly feel a suction. Although we discussed how I open and close damper doors, I realized later that he never checked, opened or adjusted them during the cleaning. He could have closed all but the one he was working on in order to increase suction results. His next step was to blast air into the duct and then attach a “squid-like” device that slapped around inside the duct as far as he could reach. This is important! In a newer house, ducts have long straight runs from the furnace. In older houses like mine they can turn and twist. In fact, the duct we have a problem with runs straight up from the basement inside a wall and turns 90 degrees into a soffit for three feet then into two 90 degree turns to get into the floor joist area for another two feet and finally a 90 degree turn up to the second floor register. When he cleaned this one he could only get three feet into the register with the hose or squid because of the turns. That was the case with most. Hardly what could be described as a decent cleaning.
What if you move into a 20 year old house and find that the people who owned it previously NEVER replaced the filter? It was so dirty that the HVAC system did not work at all. For most people - duct cleaning is NOT a waste of time or money. You must not have allergies. I have very bad ones plus asthma. It makes it very hard for me if I don't get it done every few years. By the way - the ducts get dusty just sitting there - especially without air going through them. Dust settles on them just like it does the furniture.
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.