"At the time she sank, wasn't Portugal owned by the Spanish?" - Nope HMS Victory sank in 1744, the sixty year period of the Iberian Union was from 1580 to 1640.

"The Portuguese might have a claim though given that it was their gold that was being shipped aboard the Victory." - Not necessarily the link you supplied states - "The HMS Victory was returning from Lisbon, Portugal, and was probably transporting 100,000 gold Portuguese coins for merchants, according to Odyssey's research." Does go into which merchants, coins belonging to English merchants for good purchased by the Portuguese and delivered, or Portuguese merchants sending money for goods to be sent out.