The answer is that Shopify does not suggest that you look for and consolidate duplicate customers.
Because we use their customer accounts to keep track of our customer rewards program I’ve been struggling with duplicate customers for a while. I’ve come to the conclusion that the only way to deal with the issue is to address each customer only if a duplicate account is noticed during checkout. Then we make a note and we’ll take care of it later.
I would also suggest that you ignore any duplicate accounts without contact information (only the customer’s name) as they’ll just be recreated by the POS from credit card info.