If you're quantifying genetic elements that are present in multiple copies in the genome, with little variation, you can use a rather standard approach: collect representative sequences you want to study and map and count your reads against that (allowing for a higher number of mismatches than usual). An example of this would be snRNAs, that can have 10s to 100s of copies in the genome and a few nucleotide changes each.

If you're after actual repetitive / transposable elements, there are programs designed for their quantification: check out TEToolkit. Programs like TEToolkit can also give you information about families of TE.