No. Take, for example, two people working in a police station. Both are named Michael Smith -- a common name. From a human aspect, everyone "knows" each of these Michael Smiths because they are different. Some might even assign them nicknames to tell them apart in conversation. From a data storage aspect, they are given IDs; in this case, their IDs are their respective badge numbers.
So, John Doe would have a random patient number assigned to him, usually assigned based on his details or admittance. For example, a patient # might be DOEJ0001, meaning their database allots numbers for 9999 people with a last name of Doe whose first name begins with J, but more often this also includes stuff like date of birth, to create even more space.
In the case of the show though, there was only one John Doe at that institute at that particular time, so the guy knew who was being referred to.
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