You should read the paper a bit more closely.
"We should forget about small efficiencies, say about 97% of the time: premature optimization is the root of all evil. Yet we should not pass up our opportunities in that critical 3 %. A good programmer will not be lulled into complacency by such reasoning, he will be wise to look carefully at the critical code; but only after that code has been identified"
We know that cache misses are not a small in-efficiency. This has been measured & observed on many real systems as a real, systemic problem. It's why data-oriented design is currently the King of game engine world, because cache misses kill performance. It is not premature to warn against it as a general practice as a result, as that's systemic de-optimization that will likely impact the critical 3%.