yes get a good company and pay the price, I found so much dust and dirt and wood and paint chips and bugs and even bottle caps in my ductwork. I hired a major plumbing company who cleaned ductwork and i will say they did an excellent job cleaning my vent. they did miss one point in my ductwork because i still started to see dust all over my furniture and i realized that my retunduct work that was connected with a piece of sheet metal beam which was 16" across , the contractor that built my condo used a 16" wide sheet of sheet metal to connect the vent system to my return for the air to return back into my condo. The contractor should have built a 8" x16" square duct by 6 feet long to connect my intake to my return instead of using a sheet of sheet metal 16" wide by using two 3' sections by 16 inches wide. That was a shor cut which caused a major problem fir me.
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.
In addition, the service provider may propose applying chemical biocides, designed to kill microbiological contaminants, to the inside of the duct work and to other system components. Some service providers may also suggest applying chemical treatments (sealants or other encapsulants) to encapsulate or cover the inside surfaces of the air ducts and equipment housings because they believe it will control mold growth or prevent the release of dirt particles or fibers from ducts. These practices have yet to be fully researched and you should be fully informed before deciding to permit the use of biocides or chemical treatments in your air ducts. They should only be applied, if at all, after the system has been properly cleaned of all visible dust or debris.
A small number of products are currently registered by EPA specifically for use on the inside of bare sheet metal air ducts. A number of products are also registered for use as sanitizers on hard surfaces, which could include the interior of bare sheet metal ducts. While many such products may be used legally inside of unlined ducts if all label directions are followed, some of the directions on the label may be inappropriate for use in ducts. For example, if the directions indicate "rinse with water", the added moisture could stimulate mold growth.
You should be aware that although a substance may look like mold, a positive determination of whether it is mold or not can be made only by an expert and may require laboratory analysis for final confirmation. For about $50, some microbiology laboratories can tell you whether a sample sent to them on a clear strip of sticky household tape is mold or simply a substance that resembles it.