Does it make sense to visit the islands in the middle of September?Yes, I think the islands are always worth a visit, although I am not sure whether there are still some flowers in September. Around the year, though, access to the islands is time-consuming. I recommend to visit them only if you have enough time and an interest in low-key off-the-beaten-track destinations.
What, in general, the weather at this time? Is it mostly sunny, or cloudy, or windy? How low is the air temperature?
Average daytime highs are around 20 degrees. Average nighttime lows around 13 degrees. It is a relatively sunny time of the year with around 60 percent sunny days and only around 35 percent rainy days. This is relatively good weather for Hokkaido standards.