I can understand why you might find this inconsistency in the use of -san confusing. The addition of the suffix -san to a name is done as a sign of respect. The closest correlation I can think of in English are titles such as Mr., Mrs., and Miss. You would not refer to your teacher as Smith rather than Mrs. Smith. At the same time, you probably wouldn't refer to your sister as Mrs. Smith, but you would likely call her by her first name. This is why in Hiroshima we see Nakamura or Nakamurasan depending on who is speaking. Her children or other friends might refer to her as Nakamura while someone on less familiar terms might refer to her as Nakamurasan.
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