I recognize that it could potentially have negative effects on one overtime, but I see this as a fair trade off for the abundant safety and civility in Japan.
That said, a lot of people go through this when they're new to Japan. People are so unusually polite/friendly that it makes you self-conscious of your own habits. Eventually you become more familiar with what you're seeing, and you're able to relax and be yourself. I think it took me about six months to stop worrying about offending people -- perhaps not coincidentally, this is when it became easier to make Japanese friends.
(Also, it's essential in order to learn the language. You have to be willing to barge ahead with communication, regardless of politeness. This is still a challenge for me.)