There may be slight amount of misreporting. But that exists more or less everywhere, thus it evens out IMO. In my experience, both low crime rate and long life expectancy seems more or less true.

Source: lived in Japan

There was apparently significant fraud related to the pension / social security system where people where not reporting people dead for years.

This is certainly reason to doubt it; or at least specify that this is a self reported statistic when singing Japan's praises.

Well it's self-reported in the US and EU as well. Unless you can establish reasonable grounds to believe the statistics are significantly wrong, refusing to believe them just sounds nihilistic.

nihilistic? As in "rejecting all religious and moral principles in the belief that life is meaningless"?

In any case, what's to believe? We're comparing stats here, so we have to consider that maybe this isn't a legitimate exercise in the first place. Like comparing UK sexual-assault statistic in order to derive a ranking. Without a basis for error, our conclusions may be poor.