Honestly, I am surprised that anyone would be surprised by the conditions described in the article.
(Most) eggs in Japan are extremely cheap (for the nutritional value they offer). And whenever animal products are cheap it should be clear that the animals have to suffer. Because that is what mass production leads to.
You can find free range eggs (放し飼い卵、はなしがいたまご) in some supermarkets though if you're willing to pay three times the price. Knowing that in the EU the "free range" label only means that the hens have an allocated space outside (of the factory) that they can access for a certain amount of time during the day, I don't believe the advertised promise of Japanese suppliers that the hens actually run around the farm as they wish but at least they don't keep them in cages where they can barely turn around... or so I'd like to believe for the price I pay.