In practical terms, it's up to whatever country confronts them to do what they want with them. There's not really an international tribunal for pirates.

One solution is that large commercial firms hire their own armed security, not having to rely on help from a nation getting there in time. That raises its own problems though.

Most of the time, they aren't necessarily out to kill for the fun of it. That's not the purpose of being a pirate, they want the loot, or they want the boat, or they want ransom. There are some exceptions, some of the worst aren't necessarily ocean operating pirates, but pirates on river channels or river deltas near the coasts like in Asia. Those guys might take your stuff and kill you for the fun of it, they're not after ransom or large ships but whatever some poor people or ignorant tourist who wanders nearby have in their pockets. They're not likely to get much, so the economics aren't as 'sensible.'

A terrorist on the other hand has motivation that's not profit driven. They don't blow something up or shoot up a market place for money, they do what they do for ideological reasons.

Personally I think organized crime beats hijacking ships insofar as the human and economic costs are concerned. They murder daily, extort, hijack, kidnap, rob, but It goes one better in terms of undermining society by bribing officials, operating legitimate fronts as a cover, smuggling contraband and illegal nationals, penetrating and controlling the prison system, or getting involved in large scale commercial crimes- wire fraud, credit card theft, identity theft and human trafficking rings. It's not as dramatic or attention getting perhaps because warships don't often come into contact with it, plus it's more mundane as it's more everyday and just sort of accepted.

Great care has to be taken in case their human rights are violated.

Don't worry, they have lawyers from YLS.