Pirates on F.I.
 

There are some free-roaming pirates (these in ships) on Freedom Islands. I can talk to them, and basically it's a joice between fighting them or paying a fee.

Are they any quest-related or something like that, or I can defeat them like any other stack of monsters?

There is no quest for the freelancing pirates, but there is one for a harbored ship - it is able to attack this ship at night, but in the day you will receive a good quest... so it is better to get the quest first :) only if you would like to have one more battle and one less quest... :)

also when you mentioned "attack them or pay them a fee" there is always option to just set sail and get on a run for free :)

I guess you mean that cursed captain and his crew. I just talked to him, he promised some Ruby for litfing the curse. If i fight him afterwards do I miss anything else?