What is stopping the "captain" from taking a little detour to the English country side, better yet, New Zealand, and kidnapping a few farmers?
Why? Well, apart from the possibility you mentioned (which is unlikely -- just you try committing piracy on British soil in the 19th Century in a ship with its name and identifying information written on the back), there was presumably the possibility that a captain might let a prisoner escape in exchange for money. Also there's the problem of maintaining security on the prisons. And finally, I'm sure there was a constant need to cycle guards as well as prisoners back and forth from Britain to the colonies.
I doubt many merchant captains had the forces necessary to kidnap large numbers of people anyway. Besides, It would have been much faster and more profitable to just go straight to Van Diemen's Land and drop off the 'cargo.'
All I am saying is, counting the cargo is not the most ideal solution for the Murdering Captain problem.
Sometimes you might even get willing participants. Say, a ship paid to transport 100 Cubans to the U.S for political asylum might just be better off bringing 100, paying Costa Ricans (ignoring linguistic identification :-)
I have an academic interest in this because I have been a refugee escaping on a boat, helped by traffickers to leave Somalia. And also, because I have an interest in the accurate identification of undocumented individuals (with their active participation, of course; adversarial identification is something better left to Langley)
Survival stories are not worth telling if they're widely shared and experienced. In fact, there are people in New Orleans who have had it worse than us. Because of that, I prefer to be silent, and grateful.
Plus, historically, at the time, New Zealand was not a penal colony like Australia. But home to the English gentry.
(I have the Australia Almanac and it's full of interesting tidbits. One of them was when I read "The English met with the Aborigines during a time of hunger .. 5 men where eaten". I shook my head briefly at the inhumanity and went on to read .. then paused, and re-read the passage again. Turns out, the English ate the Aborigines.)
Whether the Aborigines ever engaged in cannibalism was a somewhat fraught political topic in Australia a few years ago. (The answer is "probably someone got eaten by somebody at some point in the 40,000 year history of the thousands of Aborginal tribes, but you're not supposed to talk about it.")
Anyway, the story isn't about captains "recreationally murdering" prisoners, which is the kind of thing that only a tiny number of psychopaths would do. It's just about them failing to take quite as much care of them in terms of food, water and medical treatment as they really should have.
As for cannibalism, my profile info has been a passing reference to it, in jest; it doesn't concern me at all, at least not until the zombie apocalypse (if food rations run low, I might have to hunt a few zombies and raid the mall shops for flat-screens and warm Heineken!)
I'm filing this under "extraordinary claims demanding extraordinary proof" for now.
The wealthiest and most powerful families of that era, or any time before 20th century, had difficulty identifying kins and heirs. The whole study of Genealogy (and, perhaps the institution of marriage!) was created for the secure identification of blood relatives and safe transfer of property.
Even visual identification is spotty when IDing strangers.
All in all a pretty high negative incentive (which it had to be, to keep starving people from committing crimes).