That is what is alleged, but has yet to be proven.
I doubt that the owners put up billboards or bought ads saying "Store your ill-gotten goods here, wink-wink". It is much more likely that the business was taken advantage of by criminals. Like how FedEx and UPS are used to ship drugs.
Judging by the lawsuit, there's at least 400 customers who used them for legitimate purposes. And some unknown number of customers who used them for nefarious purposes. At what percentage nefariousness does a business become a criminal enterprise, resulting in a large raid by the FBI? Sweeping up and inconveniencing the innocent customers in their dragnet?
Traditionally, the answer was "your bank", but does that apply anymore? Chase is discontinuing the service, I'm sure plenty of banks never offered it in the first place, plenty of people use "online-only" banks where there might be a branch for legal reasons, but it's nowhere they could easily stop in and retrieve documents, and entirely too many people are unbanked.
This seems like enough of a gap in the market that a third-party service that says "we've got a really secure building with armed guards and lots of cameras and stuff" could reasonably find an audience among the law-abiding.
I assume a service like the one raided doesn't advertise to the broad public "store dirty assets here" -- indeed, one would expect advertising the service to non-criminal customers would be an important part of their legal ass-coverage strategy.
Anonymous safe deposits threaten the paradigm that assets should by KYC'd and easily visible to creditors/the wife/child support/.gov/privacy-hating-tyrants without resorting to depending on the testimony of the defendant.
Saying "anonymous boxes are a problem" is viable if there's a prominent non-anonymous alternative. I don't think that exists-- see my concern about the bank option.
Hell, one would think this would be a great opportunity for law enforcement to get a direct line into "normal people's" business. Let them do a safe-deposit service: put my passport/birth certificate/old paper stock certificates in a vault at the police station. It's less likely to be burgled than my house, and if they want to gawk over a 30-year-old certificate for one share of MCD, they can feel free.