Yes, and that is likely to happen again unless the vessels sentry systems are awake. The threat level is ramped up if the pirates think that they are liable - for one reason or another - to escape with their lives - others won't care either way.
Perhaps a part answer might be an exclusion zone of around 1,000 yards with the ship at the center. Any suspicious object entering gets a warning, maybe two. Then obliteration.
It's pretty certain that a determined attacker will be effective. Even a drone with a pound of Semtex strapped to its underside will create more than a big bang.