Most software done by bio"informaticians" seems sub-par, both in implementation and in theoretical properties. I'd suspect this is caused by the fact that a lot of people actually don't come from CS, but biology or other fields.
https://en.wikipedia.org/wiki/Rabin–Karp_algorithm
Rabin karp with rolling hashes is actually (not exactly but almost) what tools like rsync, or bittorent use to find chunks and differences in files. So it scales really well.
The algorithms you cite come from a time when computers looked rather different in their architectures.
Linearly scanning the entire genome from ram for example, could be significantly better than performing multiple index lookups from disk.
Many problems of bioinformatics (the text processing) aren't that hard or special anymore, a genome is tiny compared to the amount of data we have lying around elsewhere.