We have a customer who has multiple LLC accounts. Do we aggregate those deposits for CTR purposes? Does beneficial ownership change anything?

The guidance on CTR aggregation did not change with the new CDD rule and beneficial ownership.

From Question 32 of the FAQs issued in April 2018:
With respect to legal entity customers that may share a common owner, unless there is an affirmative reason to believe otherwise, covered financial institutions should presume that different businesses that share a common owner are operating separately and independently from each other and from the common owner.

...financial institutions should not aggregate transactions involving those businesses with those of each other or with those of the common owner for CTR filing.

Aggregation for a common transaction conductor would follow normal aggregation rules.