I'm not sure how much of an advantage they gain from having very easy port access by virtue of being an island (probably quite a big one, I assume). But it is hard to accept they wouldn't be having a much easier time if they had easy access to something like the Saudi oil fields, the US oil fields, the Chinese coal fields, etc etc. They are a long way away from the good sources of natural resources.
And they struggle to be self sufficient in food in the first result I found [1]. That is pretty different from somewhere like the US. There is a real risk of war in East Asia, so I imagine they'd be quite uncomfortable with that.
They have completely different resource-use problems than the economies that are larger than they are. The idea that the US would have to exert itself to be self sufficient in food is rather weird, as is the idea that China would struggle to justify transporting resources to the country from Mongolia, etc. It is obvious to me what could be done with more people in the US or China. In Japan there is probably something, but it does require actual ability to find instead of just "dig more, grow more, build more, forge more" that their competitors for the best-economy crown can manage.
Japan needs transformative technological improvements to grow. The US needs warm bodies. China needed to stop the Great Leap Forward and put competent leaders in charge. The Japanese challenge is much greater.
[0] https://en.wikipedia.org/wiki/List_of_mines_in_Japan
[1] https://en.wikipedia.org/wiki/Agriculture,_forestry,_and_fis...
Your counterargument is that they didn't have a problem in 1980, when they had less people and the same amount of land. I can't disagree with that, but it isn't relevant.
> Many, many other countries don't have a lot of natural resources and are not having these problems.
They have the 3rd largest economy in the world. It goes US, China and then Japan. 30% higher GDP than the next contender, Germany. If there are any non-linear economic effects at all between size and labour market, Japan is going to find them first.
And the chart in that article shows that they basically stopped having children in 1980 which would be consistent with a "running out of resources" hypothesis as a root cause. If they hit a wall in economic carrying capacity circa 1980 that chart would supporting evidence.
But concerning the actual topic at hand, Japan's labor market problems have nothing whatsoever to do with a resource or land shortage.