Sorry, but it's a sign of a justice system very out of whack and not something to defend.
People are only okay with it because most people don't have any interaction with law enforcement, let alone the justice system.
I was in no way defending that system at all. I was just pointing out that the 99% statistic is constantly thrown about in Ghosn discussions without ever mentioning what the conviction percentage is anywhere else. And if you use the US as a a standard of comparison then that statistic is actually quite high as well. And if use the same calculation as Japan then the US is also above 99%.
If someone says "the life expectancy for women in my country is 88", then without comparing that to somewhere else perhaps your own country then you don't really know if you should consider 88 high or low or normal. Anyway the link I provided discusses comparative justice systems and why this is, including your first point.
What I managed to find easily just now in https://www.justice.gov/usao/reading_room/reports/asr2012/12... page 9 has: "Of the 87,709 defendants terminated during Fiscal Year 2012, 80,963, or 93 percent, either pled guilty or were found guilty."
So quite high, but not anything like over 99%.
This is federal cases, though, so maybe state cases have higher enough volume and conviction rates to make the overall number over 99%? Again, I would love to see hard data.
[0] https://thediplomat.com/2020/03/carlos-ghosn-and-japans-99-c...
Edit: looking at your linked PDF I think the above quote is missing the thousands of misdemeanors dismissed by judges. This just goes the show the difficulty of comparing legal systems using a single number from each.