I echo most of what has already been said. This is a round and round good throw in plot for any scenario. It can even work in a sci-fi setting like Firefly, Fading Suns, Babylon 5, etc with minor modifications. Such is the role of a good sub and plot. (just for thinking that I threw in another .5 for its functionability)
To me what makes this such a good plot is not that it is a basic, enter bad guys, thwart bad guys, find out good guys could be actidental bad guys due to motives but that it could be a one or two shot side plot thrown into a much larger game or it could turn into a grand scenario when the players only intended to stay for a few days in this waylaid town. Kudos.
Plots (Nature) (Single-Storyline)
My own take on this is that it should work well as a subplot in developing a broader politically-motivated setting. It's not much on it's own, but it is decently structured: Opening fireworks, then some background explanation that actually seems to work, then some decent role-playing opportunities. I just don't know what would happen once the pirate ship is discovered: The PC's might flee for home and cause a war, or try sabotage - and likely get themselves jailed or killed.
This plot never came to fruition in my campaign - the party quite literally self-destructed while following the Zellin up the coast, and we reset to a different set of PC's in a different part of the world to minimize the fallout. Two years later, my players started asking "whatever happened with the pirates". Sigh. Go to Comment