"Others have written with concern regarding the harsh secrecy provision in the statute which includes the risk of criminal penalties for those lay judges who would publicly share confidential deliberation room discussion even after trial proceedings are complete.:
I'm sure there's a lot more where that came from, plus of course as you note extreme deference would likely be paid to the professional judges. The above is from the end of https://en.wikipedia.org/wiki/Lay_judges_in_Japan
https://en.wikipedia.org/wiki/Yoshiyuki_Kouno
The investigation of the Tokyo sarin attacks, on the other hand, seems to have been carried out pretty much by the book and I'm not aware of anybody outside the tinfoil hat brigade who contests that they got the right people.
http://news.bbc.co.uk/2/hi/8290767.stm
Police can hold suspects for 23 days; those interrogations are private; Japan only recently re-introduced trial-by-jury (2009!); etc
Here's a nice 28 minite radio programme talking about the problems. http://www.bbc.co.uk/programmes/b01phktd
[1] http://www.nytimes.com/2007/05/11/world/asia/11japan.html?pa...