Air conditioner size is measured in “tons.” However, the tonnage of an HVAC unit is not actually based on its weight. A “ton” is simply a measure of an air conditioner’s ability to cool your home. One ton is the ability of your air conditioning system to cool 12,000 BTUs (BTU stands for British Thermal Unit) in an hour. Likewise, a “2-ton” central air conditioner is able to cool 24,000 BTUs per hour.
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.
There are many interesting comments from several informed individuals. The question that has not been answered is how do duct systems get dusty and dirty? As a RESNET Home Energy Rater, I perform pressure tests on homes and duct systems, and the one common thread is . . . most air delivery sytems have large amounts of air leakage. The solution is to seal the duct system, and pay particular attention to the return duct system and ductwork near the air handler (the 'blower'). As others have said, a captive (sealed) duct system with proper filter maintenance should be more then adequate for most occupants. For those who have allergy, asthma, or other breathing problems, a filter with a higher MERV rating (number should be listed on the package) or a HEPA filter are good choices. These filters will capture smaller particulates and should improve the indoor air quality. Again, make certain that the entire duct system is sealed, preferably with mastic, second choice UL-181 foil tape - never use cloth duct (also known as duck) tape.