It's unpredictable that late in the season. Last year was fairly wet. The year before was hot and sunny and we were on the beach or by the pool on Oct 19th, when we left.
It can get cool in the evening.
My advice would be pack for all eventualities, and be sure to have rain-wear. It's a great time for walking - far better than full summer heat - so walking shoes are a good idea.
Some tavernas will close and many sun-beds on the beach will migrate to their winter homes, but there will always be plenty of places to eat and drink.
Others will probably disagree, but I think that you should plan where you're going to stay taking into account the fact that if it does decide to rain with hurricane-force winds for a few days and you are way out from anywhere to eat it could be less than joyous unless you have a car. Good places to stay would be self-catering apartments that serve food, of which there are many (Romanza, Vikki, Athina, Barras, Little Prince, for example). This is also a good time for half-board. When the weather closed in and we were at Nafsika we didn't need to get wet, and the inmates (sorry, guests) developed a nice sense of British WWII survival community spirit sitting in the bar with Spiros leading the singing of "Who Do You Think You're Kidding Mr Hitler?" (That's a lie, but it's an amusing thought!)
Go expecting the worst and then every gorgeous day feels like a gift from the gods. The sea is usually warm, and the sunsets can be spectacular if there are storms out to sea. The food remains fantastic and the beer tastes just as good.
We'll be back in late September for the third year - so you can tell that we love it.