The story said they were making cash deposits from $500-$9000. The lower limits shouldn't be a problem at all, especially considering their business. My guess on the $9K deposits is that they were made on days when they had more than $10K of cash.
They may have simply thought the same as a lot of people - that keeping a deposit under $10K means no paperwork. They, like many people, may not have known about structuring and just wanted to keep the government out of their beezwacks. These days it seems there is less chance of scrutiny with three $50K deposits in a row versus three $9K deposits in a row. Better to just do the paperwork, though I'm completely sympathetic to law-abiding people who don't want to, or feel offended, having to fill out paperwork intended to catch drug pushers and terrorists.