That's probably an excessively high conviction rate and includes at least some bogus confessions, possibly due to cultural reasons, but I wouldn't overestimate that. Most jurisdictions in the U.S. have conviction rates easily in excess of 90% too. The simple fact is the vast majority of criminal defendants are, in fact, guilty.
Well, depends on how you look at it.
In Japan, you can hold a suspect of a crime for up to 23 days (48 hours at the very least), during which you either have them spill they did it or find proof that doesn't require their confession they did it, so long as you have enough burden of proof you can present to their version of a prosecutor that presents probable cause to consider them a suspect worthy of detainment for questioning, in which case the detainment can last up to ten days to the max of 23.
This means they can legally leave you in a cell for about a month, with the only breaks being interrogations, during which they must let you go at the end of that interval if you don't crack and they can't hang any flesh on the accusation without your cooperation.
Your ability to retain legal counsel is somewhat worse than in the U.S, as in their culture if you are accused of a crime, it's generally assumed you did it and the defense attorney is trying to get you a fair plea bargain most of the time, unless you can present ironclad proof of your innocence.
Generally speaking, while in both Japan and the U.S. they can pick you up for questioning, they only hold anyone 48 hours for any reason whatsoever in Japan, only up to 10-23 days if they can convince a prosecutor of the solidity of their case against you after that.