From reading about this issue and my own experience, I've found at least two things to be quite consistent with quest lines. Probably dating back to the disney design. When one gets a quest at sea or land, if the npc didn't specifically instruct you to do things in a certain area, then whatever the items are, they are almost always found in the general area of the quest giver if no real clues are given. If ships, then near the island or main area of quest giver. And in what I think is logical, the item is made more of a challenge within the quest itself.
Ships become scarce, but almost always turn up near the area of origin. It may have took longer, but the item appeared at some point.
I think when people wander away from the origin, if not given instructions to do so, traveling away may effect the reset time of items. Ex: If your item is in a fort and you run around looking for it, and it should show up in say, 4 minutes, but you exit the fort at 3 minutes, it may reset each time you return to the area. So if you keep moving away, perhaps you're never there to see the item, and or you reset the time yet again.
I can't say how this game handles quests, but this is what I see. And most complaints are by people who go all over the place looking for something.
I say this because I believe tlopo like most games, recreates your space as you go, and if you leave, it has to rewrite stuff over again for what your world looks like to you as you move. Perhaps this process if even half true may wipe out something as it goes.
Just throwing that out there.
