Disclosure: work in japan
What I have realized talking to the native people here is that working late is due to :
1. Impress peers and managers 2. Impress wife and her friends that you are important to the company 3. (For people with young kids) Not be a nuisance to the sleeping schedule of kids by coming early 4. Nothing much to do after going home because of lack of intimacy with spouse/partner 5. Actual work requirements 6. To earn overtime pay since basic pay is too low to cover all the expenses.
People have different reasons at different points in time.