Because the why can be completely unrelated to the code (odd business requirements etc). The code can be known to be non-optimal but it is still the correct way because the embedded system used in product XYZ has some dumb chip in it that needs it this weird way etc. Or the CEO loves this way of doing things and fires everyone who touches it. So many possibilities, most technical projects have a huge amount of politics and weird legacy behavior that someone depends on (including on internal stuff, private methods are not guaranteed to not be used by a client for example). And comments can guard against it, both for the dev and the reviewer. Hell we currently have clients depend on the exact internal layout of some PDF reports, and not even the rendered layout but that actual definitions.
Again, if it's a comment saying "we need this hack because the hardware doesn't support anything", I don't call it "literate programming".
Literate programming seems to be the idea that you should write prose next to the code, because code "is difficult to understand". I disagree with that. Most good code is simple to understand (doesn't mean it's easy to write good code).
And the comments here prove my point, I believe: whenever I ask for examples where a comment is needed, the answer is something very rare and specific (e.g. a hardware limitation). The answer to that is comments where those rare and specific situations arise. Not a whole concept of "literate programming".