The number went up from 1500 last year to 2100 this year, so not a strong increase in absolute terms.
And the only reason why that's more than the Coronavirus deaths is because they have managed the pandemic quite well so far, like - it seems - most Asian countries do.
To put things into perspective, the monthly suicides in Japan from all reasons combined is about the same number as 4% of the monthly US coronavirus deaths.
So while sad, Japan increasing their suicide rate by about 0.005% of their population per year sounds like a good tradeoff against risking a >1% death rate.