Japan in June

Is late June-early July (ie 30 June-14 July) a good time to visit Japan or is it too wet to make is worthwhile?

I think it is OK to come to Japan. Indeed, it is in the rainy season but it does not mean that it rains all day long and the rain itself is not a shower but a drizzle.

There're some places which are more beautiful when it rains and hydrangea is in full bloom.

It's a great time to visit, the rain won't impact on your time here ... like Jlady says, it's a drizzle, not necessarily a down pour you may expect.

Icic. Thanks for your replies. Indeed I thought that it would pour with rain as other parts of Asia during the rainy months. Is it very humid though during that time? Would mid September be a better time to visit?

The further south you get the more humid it is in June and July. When the rainy season ends, it begins to heat up and head into the typhoon season. It can be humid depending on what part of Japan you're visiting in September, and you may have an occasional typhoon then which can stop trains and ferries. Tohoku and Hokkaido are a bit cooler and they also don't experience the rainy season stationary front.