My fleet brings back random stuff like cabnets and instruments and in shops you can spend money on idols and other strange stuff, but seeing as how that stuff doesn't seek to appear in your boat where is it? What is this for? Is it on display anywhere? Do I get like a pirate hideout later?
...he takes you to the room under the mansion filled with treasure, up some hidden stairs into your mansion where he shows you the Templar armor.
These aren't side missions that are missable. They are main plotline missions. If you are using the diving bell already (which doesn't appear until sequence 6), you've already done them already and have had The Cove, the mansion, and its associated town, which all need various degrees of upgrading.
You missed all of that???
There's no zodical sign called Nesbitt. GT: Dr Nick 1971