Why the words get flipped
English questions in the present simple need an auxiliary verb: what does SEO mean. Many other languages build the same question without one — German says was bedeutet SEO, French says que signifie le SEO — so the auxiliary disappears when the pattern is carried across. The result, what means SEO, is a direct translation rather than a mistake in understanding. The person asking knows what they want; only the grammar is non-standard.
There is a second reason the phrase survives. People type quickly, and "what means seo" is three words instead of four. It shows up in autocomplete, in forum titles, in chat messages from buyers who are not writing an essay. For a business, that matters more than the grammar lesson: a real person types this, so a real page should answer it.
One more note on the noun. SEO is an initialism, read letter by letter, not a word like "laser". That is why people write search engine optimization out in full when they define it, and why the same question arrives in several shapes: what means SEO, what does SEO mean, what is SEO, and what does SEO stand for. All four lead to the same answer, which is the one in the box above.