I guess that there are some plot holes. You are right, it is strange. The goblins know that they are allied with mindflayers and want to kill anyone who attacks a mindflayer. They don't know that they have tadpoles. Gut talks about shadows. She knows that there is something in her head but she does not realize what it is. I guess some kind of spell or suggestion prevents them from understanding that they have parasites. I think that the cras stopped the mindflayers and they could not finish the process. So the people on the ship were likely supposed to become true souls but the process was interrupted. Anonther possibility would be some kind of mindflayer civil war. The one side creating true-souls and the other one creating tadpoles that can initiate immediate conversion into mindflayers.
2: They must be or the True-Souls would transform into mindflayers. The process should be complete after a week and with all the long rests the game takes longer yet none of them transform.
3: It would appear that there is no relationship. These items only work on those branded, I think there is no indication that the tadpole mediates their power. We will see once we get a non-tadpole companion.
I sometimes use thought experiments. I don't necessarily believe in every idea I post for discussion on this forum