If a merchant ship encounter a pirate hijack and ask for USA Aircraft to rescue, does the Marine Shipping need to pay for that？

It depends. If it was purely a pirate hijacking, probably not. Put if the merchant ship did something they were advised against doing that contributed to the hijack, possibly.

No, the principle is enforcing the right of peaceful navigation so it's no charge. It's not really a cost to the taxpayer, because aircraft time and so on would be used up on exercises if they weren't doing actual operations.