I've been in business in Florida for 25 years and purchased a $12,000 duct cleaning system 4 years ago. In the last four years I've cleaned 5 duct systems charging around $400 each. Not a very good return on investment. What I have been doing most the time is I get a call by someone panicked because they called some low priced company to inspect their system and were told they have dangerous black mold. Then they call me to have a look. Most the time they don't have mold, ducts look very clean. However the coils are dirty and the inside of the air handler cabinet needs cleaning. Keep in mind not every system can handle supper high efficiency filters! These filters can block air flow quite a bit right out of the package. Many older systems can't handle pleated filters due to increased static pressure. "Back rooms with low air flow". I have taken many hours of classroom study on indoor air quality. Never got any certification because I don't want to pay another organization dues yearly. I think the problem with duct / system cleaning is most people are suckers for low priced scams that are rip- offs . People call me all the time and ask how much? When I tell them average $400 they hang up. I know I do the job correctly and honestly, and they are going to get racked over the coals by the scam artists by calling $79 whole house duct cleaning guys. People need to check internet, angies list and BBB reviews. But keep in mind even reviews need to be sifted through your rational person filter.
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.
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.
To find companies that provide duct cleaning services, check your Yellow Pages under "duct cleaning" or contact the National Air Duct Cleaners Association (NADCA) at the address and phone number in the information section located at the end of this guidance. Do not assume that all duct cleaning service providers are equally knowledgeable and responsible. Talk to at least three different service providers and get written estimates before deciding whether to have your ducts cleaned. When the service providers come to your home, ask them to show you the contamination that would justify having your ducts cleaned.
I am NADCA Certified Air Systems Cleaning Specialist. Over the years I have learned on simple answer to this questions: there air duct cleaners and there are pretenders. There will be no benefit at all if you use on the very cheap pretender because they will not really clean anything. On the other hand if you call a qualified air duct cleaner with a NADCA Certification you will, like 99% of my customers, report improvement with your respiratory problems, you will see less dust and the job will pay for itself with energy savings and repair prevention.
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.