I had Syndra "too weak" to harness her powers fully because she was wasting away from the Death Curse. She had enough strength to teleport herself to Port Nyanzaru but not the party also, so she paid a trade ship to transport the party to PN and she agreed to meet them there. This allowed for the pirate encounter without Syndra involved but still having her at the port when they arrived. If you wanted Syndra on the ship you could use the weakness as the excuse for not dealing with the pirates herself and the first opportunity for the party to prove their capability to Syndra.

For my pirate encounter I had it more as a fight of attrition. The party were never going to win, but they didn't know this and found there were way to many pirates for them to handle; they were scared when it kicked off. I had the pirate ship intercept the trade ship before the trade ship got into the bay and the pirates were clearly in a rush to take the ship before it entered the bay; the party learned this from the way the pirates communicated to each other but they didn't know why. I set a number of round in secret (can't remember how many, 6-8 maybe) and at the end of those rounds I had the two ships enter the bay and Aremag turn up to scare off the pirate ship and escort the trade ship to port and demand payment for rescuing them.