A former owner where I did some repair work had evidently tried to keep the rodents out by nailing a flattened tin can over their entrance. Mice or rats I never determined, but they chewed right through that makeshift cover and continued to use the rafters as they wished.
At a minimum I would recommend T&G plywood and hope they wouldn't be able to detect any warmth from above. When the cold season comes they would make short work of 3/4" plywood.
There are some concrete based 4'x8' panels that besides being heavy might be better at keeping them out. Of course mice will be a lot easier to stop than their larger cousins.
An abundance of traps to eliminate them before they start chewing their way in is always a good defense. I try to avoid poisons and local domestic animals might be affected.
If your ducts are below the bottom sheathing I would wrap them or box them in with metal.
The ducts are below the floor and above the dirt under the houses. It sounds difficult and expensive to wrap them or box them in with metal.
mothballs have worked for decades
You have to keep it out of their reach thus a Sealed crawl is the best option
For a vented crawl, make sure all your insect & rodent proofing is in place also; Using flex duct is not recommended, nor fiberboard, just metal ducts sealed with insulation on the outside. Better to have to make a few cosmetic repairs occasionally then let them get into the system.
If an existing issue, how are they getting in, in some cases it is from above & that needs to be dealt with also: http://blog.sls-construction.com/2010/safety-sunday-rodent-prevention
We have used hardware cloth (1/4" mesh wire) and then sprayed it with single part foam. I have heard of used cat litter (urine smell) sprinkled about and moth balls as other options.