Should you avoid Japan during Golden Week or peak cherry blossom season?
Not always, but do not stumble into those periods by accident. Peak season can still be beautiful, but accommodation, trains, restaurants and famous sights need more discipline.
Answer
Peak Japan is not automatically a mistake. Cherry blossom season can be lovely; Golden Week can be manageable if you understand what it does to domestic travel. The problem is arriving as if it is a normal week. Prices rise, availability tightens, famous places crowd early and spontaneous route changes become harder. If you are travelling then, commit: book key transport and hotels early, reduce hotel changes, avoid stacking the most famous sights at the busiest hours and leave room for quieter neighbourhoods. If you do not care deeply about that timing, shoulder periods can give you a better trip with less effort.