You're right, "nothing has changed since he met him" is correct when you're talking about up till and including right now.
When talking about a point in the past, sentence 2 sounds correct. Because the simple past is used with the present perfect (hasn't changed since they met), using the same simple past with the past perfect sounds odd. Therefore, "nothing had changed since they had met" is talking about a time in the past that does not include the present, because something might have changed between then and now, like in "nothing had changed since he had met him, until they took a vacation together" (and since then, things have changed).
(not a teacher, just a language lover)
Student or Learner