The better one is Digital DNA-DNA hybridization only but its bit expensive as compared to the manual one, in digital we need to have the whole genome of all the species. Let's say you need to analyse among 3-4 closely related species than you need to sequence all the 4 species than only and its bit expensive. But the result form the digital hybridization can not be compared to the manual one as it is very accurate.
where as the manual hybridization needs the experiment in triplicates to give the real picture.
Thanks for the comment.