Japan usually seems very strict about hygiene and regulations, and since it’s a chain, I think this seems a lot bigger of an issue than it is.

If I had to guess, a central warehouse has had evidence of vermin (after the mentioned rat miso soup at one outlet and a bug in another outlet), so instead of being like “oh well we’ll see if anyone sues if they end up noticing they’re eating cockroaches”, it’s probably a matter of honour to the company to just get rid of anything that could even with low probability have the slightest contamination, and the company ofc eats the losses and doesn’t whine and actually deeply apologises and reassures customers.