Trip to Miyako Island from Tokyo/Haneda?

So, me and my friend are coming to Japan 6th of September and staying for two weeks.
And now we're thinking about visiting Miayko Island and asking advices from you guys. We would like to know pretty much everything you want to share with us.
We know September is the typhoon season, but is there really so many typhoons that we shouldn't even think about going to the islands? We're from Finland and we don't have thosekinds of storms here so we don't know..
What about plane tickets? Should we consider buying the air passes example ANA Group is offering or just get tickets from the airport?
There's couple of question we'd like to have answers to, but anything you want to tell us, we'll appreciate it!
And just you know, this is our second trip to Japan so we know something already about culture etc.
Thanks!

And now we're thinking about visiting Miayko Island and asking advices from you guys. We would like to know pretty much everything you want to share with us.

My knowledge about the island is summarized here:
http://www.japan-guide.com/e/e7300.html

We know September is the typhoon season, but is there really so many typhoons that we shouldn't even think about going to the islands?

No. On average there are 1.7 typhoons in Okinawa Prefecture in September. Not all of them hit Miyako. So, in average, typhoons are responsible for probably 2-3 days of bad weather in September. Apart from these, September comes with generally good weather in Miyako (60-70% sunny days).

The problem of typhoons are their impact on flight schedules. I personally would avoid using the low cost carriers and use an airline which takes proper care of their passengers in case of cancellations, such as JAL, ANA or Skymark.

What about plane tickets? Should we consider buying the air passes example ANA Group is offering or just get tickets from the airport?

Direct flights to Miyako tend to be very expensive unless you are able to use an air pass. The passes are explained here:
http://www.japan-guide.com/e/e2364.html

It is often cheaper to take a cheap flight to Naha and then a connecting flight to Miyako.