Perhaps there is hope yet for using RAD to estimate genomic copy number and allele frequency of duplicated loci; see this approach from cancer genomics. It compares RADseq to exome and whole-genome sequencing for estimates copy number and allele frequency of duplicated regions.
That said, they have access to resources we don’t (i.e. a full reference sequence), and collapse adjacent sites, but at least it is a start.
Caihong Zheng et al.
Determination of genomic copy number alteration emphasizing a restriction-site based strategy of genome re-sequencing
Bioinformatics first published online August 20, 2013 doi:10.1093/bioinformatics/btt481