1. Probabilistic filtering and matching: Since you mentioned bloom filters - other probabilistic data structures like count-min sketches (roughly, streaming bloom filters) are super useful. Approximate kmer methods like minhash and w-shingling use them in really cool ways. Rolling hash methods like Rabin chunking also work really nicely with probabilistic/streaming hash tables - splitting the data stream into chunks…
Basically, it makes a similar point to https://news.ycombinator.com/item?id=32186837 — i.e., cache effects are not modeled in big O analysis, even though most problems that involve large amounts of data (so most problems) are memory bound rather than CPU bound. The blog post makes a good case for a very simple hash table as a better fit for this problem.