That’s a really good question, and I look forward to the dialogue on this.
First, there is the distinct possibility that the PCs buffed the ship up before leaving Sasserine. They certainly had the opportunity and, depending on how things were going, they may have had the means, as well. They could have bought a ballista or two.
Now I’m going to talk tactics and if I don’t watch myself, I could eat up all of Paizo’s bandwidth. Suffice it to say that there are A LOT of variables – like a chess game. Sometimes having one pawn or not having it can make all the difference. They aren’t expecting any ships, am I right? If you have the Nixie and the Sea Wyvern pulling up on either side of one of their ships, that could be good for the marine equivalent of a surprise round, couldn’t it? Oh, and flanking.
The PCs may engage them while they are still a ways off. If they take out a few ships before they enter the harbor, imagine the morale boost that would be to the defending forces.
What if they keep the Wyvern hidden until the fleet enters the harbor and then comes in behind them. Again, surprise. If it’s both ships coming in behind them, the invaders may suspect here are more behind them. Negative morale for the fleet, maybe?
It’s a surface for the spellcasters to launch spells from, as range is a factor. Better to cast the fireball when their still a ways off so they can crisp up for a while before they even get a chance to launch their attacks.
And my last point will be to point out that this point is all on the players anyway. You have enough to worry about planning the fleet’s tactics without worrying about how the PCs are going to pull off their end. That’s their problem. Besides, you might be surprised by what the players come up with, and that’s a good thing.
Having two ships would increase your chances of getting an early warning of the attack. Here's how it works:
If you have no ships, you're basically stuck waiting until the crimson fleet ships are visible from the highest point of land on Farshore Island. If the ships sail in sight of an Olman village and the wind is pretty dead, an Olman canoe might give you slightly more warning.
If you have one ship (the nixie), you can patrol the most likely sector for their approach (northeast), with a fair chance of seeing their approach, and with good sailing you can gain on the CF ships to give more advance warning (you're probably loaded more lightly than the CF ships because they're on a long sea voyage, requiring more men and supplies) or better yet use magic to communicate to get an extra day or two of warning. Alternatively, you can patrol closer in and cover a wider sector of possible approaches--which would make advanced detection more likely, but reduce the amount of time between the CF's detection and their arrival.
If you have two ships (nixie and wyvern), you can patrol both northeast and northwest, so if the CF decides to give you the slip and come around the north and west side of the Isle of Dread you can still get advance warning. This means you can patrol farther out--maybe 100 miles out from the island. It's pretty unlikely that the CF will sail to a latitude south of Farshore and then come up from the south, because that's a much harder navigational problem, so adding a third ship to patrol that sector doesn't help you that much.
An extra two days of prep time for the assault is definitely worth 200 VP.
IMO, the two ships don't make enough of a fleet to challenge the CF in a sea battle--the PCs might take out three or four enemy ships with fire spells, but probably can't take out the whole enemy fleet before their own ship(s) are sunk by like means or captured, forcing a quick teleport back to Farshore or resulting in being adrift in a lifeboat or marooned while the CF is busy plundering Farshore.
The two ships might be of help in an inshore battle in the harbor, if cleverly employed, though they are not going to do the job by themselves. Read Forester's Hornblower series (which are very fun reading, BTW) for many examples of inshore naval warfare during the age of sail, if you need ideas.
Also, having the Wyvern makes a lot of difference t the health of the colony AFTER the attack - which is what we are measuring here. The pirate attack is the most important event in this adventure, but the victory points measure how well the entire adventure goes.