The JP server load would be different during peak hours for EU/NA server peaks - I would assume that during JP peak their servers must get extremely crowded. Also, I would assume that JP players are less likely to select EU/NA servers than EU/NA players are to do the reverse, which would also increase server load on the JP servers.

Also, I know of a lot of AU/NZ players that call the JP servers home due to the idea of lower latency.