Asking why a wink means flirtation is pretty much a question without an answer. You might as well ask why a shrug means “I don’t know”, or why “I don’t know” means what it does. Gestures are an adjunct to language and evolved way back in the mists of time.
Mind you, just as everybody doesn’t speak the same language, so too do gestures mean different things in different places. In North America, if you make the “Okay” sign (making a ring with your thumb and forefinger), everybody knows what it means. But in France it means almost the opposite; it means “Zero” or “No good”. I also seem to recall that in Italy it means something obscene, since the circle represents part of the female anatomy.
Why don’t you try searching for “gestures” on an internet search engine? Maybe they’ll give some alternative meanings for winking.
Come to think of it, a wink doesn’t always mean flirtation. Sometimes it means, “I’m not being serious”. And let us not forget the old “Wink, wink, nudge, nudge” of Monty Python fame.