Old but:

I think they wanted the main storyline to discourage you from staying there to explore (fog mechanics punishing you for getting too far away + each day ending with a “let’s go back to Narukami and give writing girl some news”) meaning that actual exploration had to be done after the quest, when the fog is definitively lifted and you see all the ghosts appear. That’s what I did, and I found them to be quite noticeable? One jumped on me as I was fishing and explicitly asked for help, another one did as I was collecting mushroom underground. The boatman is placed right next to a trial so you really can’t miss it, and through his dialogue you understand you still have people to help “board the boat”. And I just found most of the other ghosts through normal exploration.

But I saw a few people complain about the exploration being too difficult to do before the main quest is over, trying to fight the fog just to get this chest over there. So I guess the “do quest now, explore later” system they likely intended went over a few people’s head.