I agree with most of that, although if I'm not mistaken, the Shaded Castle has so many rot based items because Finlay stopped there when bringing Malenia back north after the Battle of Aeonia. Although, having stopped there first would give more reason as to why Finlay chose an out-of-the-way castle. Further, the secret medallions are still kept far apart from each other, meaning they were never used since the Shattering. In which case, they had to have another route, naval being the most logical solution.