This is the first time I have spent much time in Japan in summer, and yes, it can indeed be very humid and hot. I also suspect that sprawling Tokyo would have one of the hottest "urban heat island" effects around, and I wonder how much of that is reflected in the temperatures.
Googling the topic: hey, my hunch that there is a huge UHI effect in that city is right:
Over the past 100 years, Tokyo's average temperature has increased by about three degrees Celsius, and that of Osaka has increased by two degrees Celsius (C). Since it is said that global warming has raised the Japan's average temperature by about one degree C, the temperature increase due to the UHI effect is probably about two degrees in Tokyo and about one degree in Osaka.
Along with the UHI effect, an increasing number of patients suffering from heat stroke and other heat disorders have recently been admitted to emergency rooms. In Tokyo, the number of such patients brought to hospitals by ambulances increased to 1,300 persons in 2007 from 200 in 1996. Some studies show a correlation between deaths from heat stroke and the heat experienced during extremely hot days and sweltering summer nights.(There are lots more articles about UHI in Japan if you care to Google it.)
The good news: I was surprised at how well airconditioned the Tokyo metro trains and stations were. I'm not sure whether the above ground parts of Toyko Station are as good, though: certainly, on one previous day we were there, when it wasn't as hot as later in the week, it seemed there was inadequate airconditioning in large sections, and it was quite unpleasant. But perhaps it was just that day?
Outside of Tokyo, the humid heat (in the high 20's and low 30's quite a few days) was still fairly unpleasant for the on-foot tourist. But we did only have one day with some interference from rain, so perhaps we were lucky in that regard.
As for dressing for the hot weather: you will read that shorts are mainly for the younger male in Japan, but I think it fair to say that the willingness of middle aged Japanese men to wear them must have increased in recent years. (There were certainly many on sale at Uniqlo, too.) I regretted that I had only brought one pair with me.
And as for long, slim legged trousers: given that I have only recently acquired some relatively slim leg chinos myself (look, they may have been in fashion for 5 to 10 years already, but cotton chinos can last nearly a decade if you can control your weight - OK?) I had not realised until this trip how they make for such hot and sweaty legs in hot and humid weather.
Honestly, men (and women) who wear them outdoors in summer are fashion victims, if you ask me.
In any event, if you have a choice, I would say it is obvious that the height of summer is not the preferred time to be in Japan. Autumn and (especially) spring would have to be the pick of the seasons.