Is one of these two right and the other wrong?
If both are right, how does the meaning change?
According to the American Heritage Dictionary, 4th ed., crop is defined (p. 433) as follows:
n. 1a. Cultivated plants or agricultural produce, such as grain, vegetables, or fruit, considered as a group: Wheat is a common crop. b. The total yield of such produce in a particular season or place: an orchard that produced a huge crop of apples last year.
Based on that definition, I think that the singular crop in your first sentence could be interpreted to mean that all of the fields were planted with the same type of grain, vegetables, or fruit. For example, all the fields might have been planted in wheat. However, note that the singular crop doesn't necessarily mean that only one type of plant was cultivated. It could just mean that whatever was in the fields has already been harvested.
In the second sentence, the plural crops seems to imply that the fields may have contained different grains, vegetables, or fruit. Some might have been soybeans, some may have been corn, and some may have been sorghum, for example.
I think if you're trying to make a distinction, it will take a bit of rewriting to clarify the meaning.
(On a side note, to my Midwestern ear, "have already been emptied of" sounds like an odd way to refer to a crop having been harvested. I think I'd rewrite to something like, "There aren't many farms out here, but the crops in the few fields he does see have already been harvested.")
