EXAMPLE : At Shiprock, New Mexico, a perennially powerful girls ...

At Shiprock, New Mexico, a perennially powerful girls high school basketball team has become a path to college for some and a source of pride for a community where the household incomes of 49 percent of them are below the poverty level.

C. where 49 percent of the household incomes are
D. which has 49 percent of the household incomes

The difference is one of meaning, not of grammar (choice D is perfectly grammatical). What choice D actually means is that this one little community in N.M. has 49 percent of ALL the household incomes below the poverty level (i.e., in the entire country, or whatever is the whole universe of reference). That's unlikely, to say the least, and, more importantly, it distorts the clear meaning of the original sentence (you're never allowed to do so unless the original is nonsense).

The other thing that doesn't make sense in choice D is '49 percent of the incomes'. It's not 49 percent of a bunch of figures on an Excel spreadsheet; it's supposed to be 49 percent of the households (or of the households' incomes).