In both of these sentences the verb in the head clause, indicated, fixes the 'Reference Time' (RT, the time you are talking about) in the past. That RT establishes a time context—the linguist Renaat Declerck† calls this a temporal ‘domain’—to which closely integrated subordinate clauses are ordinarily related. At the times you are talking about:
- The approaching ship was a pirate ship. —we are not concerned with the ship’s present status, whether it is now a pirate ship or has been captured or sunk, only with its status at the time of your narrative
- The approaching person was your father. —we are not concerned with his present status, whether he is still alive or has disowned you, only with his status at the time of your narrative
This is not an inviolable rule; it may be overridden in a different context. For instance, if you are reviewing your firm’s current financial status, you might allude to a conversation in the recent past but report what was indicated in the present tense:
I spoke with Jack yesterday and he indicated that the Offenburger account is still delinquent.
Here the context is a present RT, which you drop out of only temporarily to mention your source. But in your examples the RT is clearly past: your concern is with the identity of the ship and the person at that past time.
†With various co-authors in a number of articles and books from 1989 to 2006. A brief online treatment is A model of the English tense system; unfortunately, the illustrations there are unintelligible in the html encoding.