Well about the only thing that a flying boat could fit worth taking off a typical merchant vessel would be the contents of the ships safes, some of which would not be part of the cargo thus not necessarily insured. Things like the payroll, or cash for purchasing supplies/fuel or a cargo. Nothing else is guaranteed to be worth taking. Besides seafaring has always been a risky profession, they risk their lives as part of their normal course of work
Of course there is also the issue that a flying boat with 3 crew members, merchant ship has 40-50 crew. Pirates boarding to search the ship will be awfully outnumbered, if the ship has an arms locker, pirate or two goes in after safe, finds 10 armed sailors waiting for them, now merchant ship has hostages and can just steam off. They'd need active cooperation of the ship to board, which gives the ship time to prepare whatever surprises they want
Pretty much. Immediately heave to when challenged. Wait for dumbasses to board, take two of them hostages, and lash em to the mast, then sail off flipping their buddies the bird.