a typhoon ruined 4 days out of 6
This is very unusual. A typhoon usually passes in 24 hours (in terms of closures and inability to go outside) and the weather is rarely negatively influenced by a typhoon alone for more than 24-48 hours. If it lasted 4 days, there must have been another bad weather system besides the typhoon. Or it was one of these rare typhoons that suddenly slow down for a day or two. It is not the usual pattern, though.
I think of typhoons just as an extreme case of bad weather. Bad weather can potentially ruin part of your holidays at any time of the year in any part of Japan. if it happens, it happens.
Despite the typhoons, mid June to October is the best time to visit in terms of weather. There are more sunny days than during any other time of the year.