Just like anything, there's right and wrong ways to do it. If you do it the traditional way with a japanese speaking landlord who mistrust foreigners, yes it can be hard. That is a significant portion of the market.
One thing I will say, there are real estate companies that actually cater to foreigners.
This has been my landlord for a year and I just renewed: http://tokyoeasyrent.com/en/
There are other companies like this in the space. Look on places like gaijinpot for more information like this: https://gaijinpot.com/
It's just like any real estate market, do your research beforehand.
Where I will admit it can be harder is when you want to procure a larger house. They don't tend to ask too many questions for studios (which should be enough for entrepreneurs family aside).
That being said, if you do have family, spend your time finding right place and ask for referrals.
Japan has its downsides but it's by far the best place I have ever lived (especially compared to SF) both food wise and price wise.