I visited Okinawa on two separate occasions. Once was to Ishigaki via Naha, and another time was to Miyakojima via Naha around mid-October and early November. We had a great time both times. There weren't as many local tourists as most folks are working or at school. We still booked early to secure cheaper prices of course, but none of the places we stayed at or went to felt overly crowded.
But both times I was struck with typhoons. In Ishigaki, I was almost hit by two typhoons back to back, but thankfully we had left for Naha in the nick of time and was not caught under the gale winds!
So, I want to discuss the pros and cons of traveling to these resort destination during the fall months.
Crowds? Wait Times?
Generally, we rarely had issues with crowds. In Naha on the main strip called "Kokusai Dori", there were a lot of locals and tourists out on the streets to grab a bite or enjoy the nightlife, but we never really had to queue up at restaurants. We really weren't all that picky with food, and as long as they served Okinawan specialties, had decent google reviews - we were game.
Public beaches weren't crowded at all. We never had trouble looking for parking spots as we usually started our day early anyway. In Ishigaki, there was one beach that had a smaller parking lot and it did fill up by afternoon, but it didn't really seem like people stayed long. Most tourists seem to be in the mind of beach hopping or needing to leave to find food before doing another stunt at the beach, so people came and gone in a few hours.
We took a ferry to Taketomi Island from Ishigaki, and the ferry there wasn't too crowded either. We bought same day tickets with no issues.
Unpredictable Weather
Typhoon season in Japan is typically around August and September, but in more recent times, there are typhoons hitting Japan all the way up until November. Typhoons can vary in severity; some are not more than just rain and heavy wind, while others can be extremely destructive. The thing that makes typhoons so scary is that you can never truly know how severe it turns out to be. While there are measurements for how strong typhoons are, it can change at any given moment. Making landfall often decreases its severity, but that's never a guarantee.
Either way, no one should be out in the ocean in any typhoon. And for places like Miyakojima where its selling point is its water activity, being on the island during a typhoon can be rather miserable.
There isn't much to do to pass time on the island. Miyakojima doesn't have a lot of tourist landmarks or indoor museums to visit. So in turn, you really just need to ride out the typhoon in your hotel room.
Ishigaki has a small shopping street you can visit and there are some viewpoints and landmarks to see. I personally felt being on Ishigaki during the typhoon was much more bearable, but perhaps I wasn't really looking hard enough on Miyakojima (though trust me, we have tried).