[ticking]

The method they accidentally found is not as bad as you make it to be.

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.