The time between the hijacking of airplanes and their crashing on 911 was relatively short. And once the plane was controlled by the terrorists, you knew that it was going to eventually crash somewhere. In the case of hijacking a fishing vessel at a point that was 4 to 5 hours of travel away from the attack points, would raise the profile of the attack quite dramatically. My guess is that either the fishing vessel was chartered, the captain was involved with the plan or the fishing vessel was meant to smokescreen the actual terrorist mother ship. See ya later.
They would probably have had plenty of time. The fishing boat left Porbandar the 13 November and was not reported missing until it was found floating outside the Mumbai harbour.
One can assume that the dead man aboard was the owner/captain who was killed (beheaded) once he had fulfilled his duties. Whether he had been paid or coerced we don’t know.
What remains to be found out - among other things - is whether the fishing vessel picked up the terrorists on the coastline somewhere, or if there was another larger vessel that acted as the real base of operations.
Maybe the owner of a fishing vessel was weeks ago offered a TON of money for chartering a trip if he would keep his mouth shut. Given some of the money upfront to make sure he kept his mouth shut and to keep him on board (whoops pun). After all, apparently now they don’t have to pay him the rest since his head is severed.