We have mold in our crawl space and windows, should we have ductwork cleaned?

That is usually not necessary, unless you have visible mold growth inside the ducts, there are rodents in the ducts, or the ducts are clogged with dust and debris.

The best way to keep your duct system from spreading particles throughout your home is to increase filtration at the furnace; duct cleaning has never been shown to prevent health problems. 

Check out the EPA's website for more information about duct cleaning.