In this case, the subject is 'to see you' and the complement is 'nice'. It's not 'it' and 'to see you' that are identified as being equal, but 'to see you' and 'nice'. The sentence says that 'to see you = nice', not 'to see you = it'.
McGraw-Hill Dictionary of American Idioms and Phrasal Verbs. © 2002 by The McGraw-Hill Companies, Inc. See also: (it's) nice to see you. it was nice to see you. Hey! (it's) nice to be here. (it's) nice to see you, too. (it was) nice talking to you. nice talking to you.
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it was nice seeing you meaning
