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.

I purchased one of those Amazon air duct cleaning coupons for 49.99. When the company showed up, they removed the vent closest to the air intake and immediately told me I needed $1800.00 for all new duct work. They said they could not clean the system until new duct work was installed. I thanked them and said I would give them a call. The only call I made was to Amazon to get a refund. I know I didn’t need new duct work. Be careful to not fall for unscrupulous salesmen and their pitches and scare tactics.

Heaters are appliances whose purpose is to generate heat (i.e. warmth) for the building. This can be done via central heating. Such a system contains a boiler, furnace, or heat pump to heat water, steam, or air in a central location such as a furnace room in a home, or a mechanical room in a large building. The heat can be transferred by convection, conduction, or radiation.
The HVAC installation costs below are based on residential installations only, and are priced for a single unit. Two units should be about twice the price. “Tim, shouldn’t there be a discount?” If people start giving you discounts, they are probably charging you too much to begin with.  That’s our philosophy anyway. Twice the parts and time should be twice the price from a fair contractor. The prices listed include component parts (with warranty), labor, and all materials for a complete HVAC installation.
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.
I own and live in a mobile home and was told to install a mobile home air condition well I did not want one because the ones for moblie homes are to small,so I install a home air-condidtion and its good for heating and cooling the only thing I do is change is the filter every month or two,What I want to know is how does dirt and dust comes from????
If there is stuff in the ducts, the fact that it’s laying there and not being blown into the rooms is proof positive that it is hurting no-one. The 5-6 exceptions you cite in this article I’ll buy, but only with the caveat that at least some of those could have been avoided by proper protection (during remodeling for example) – and if asbestos/lead/whatever winds up in your ducts- the remodeling contractor should be the one paying to remove it.
Do you live in a historic home and want to tie your new system in to work with existing features? The price will go up to do the job right. All of these things add up to slow down the HVAC company, which takes more time, which costs more money for labor and parts. This is especially true if they are a legitimate company which is licensed, bonded and insured. Simply put, this is the “X-Factor” in your HVAC installation cost. Again, you could get people to do it for cheaper…but you won’t be happy with the results, I promise.
I need a complete system replacement , before I was trying to get an evaporator coil replaced , of course the price is between $2200 an $2800 , then get told it probably will over tax my ac unit within months , so now and like everyone else what do you buy 14 ,15 16 17 seer units ,price and how do we know its reasonable  why can't there be '" a estimated price ,in the ball park, a range of prices ,so we can at least go from their .....  Now it's from 7500 to 15000. Frustrating  from the start so everybody good LUCK.   Draw a # from the hat    Unregulated  and who do you BELIEVE, just like on NCIS go with your gut feelin   
Duct cleaning generally refers to the cleaning of various heating and cooling system components of forced air systems, including the supply and return air ducts and registers, grilles and diffusers, heat exchangers heating and cooling coils, condensate drain pans (drip pans), fan motor and fan housing, and the air handling unit housing (See diagram).