When I place the static objects ShipLarge01 and ShipLargeInside01 in CK it all looks fine, then when I load it up in-game they are both gone. I'm trying to make some sort ocean adventure mod and these pieces are perfect, however I cannot get them to work.

I tried placing the ship at the Solitude docks and they did show up in-game, but whenever I put the pieces further North out in the ocean, they simply don't appear. Do these pieces only work in certain places? How can I fix this?

Try double clicking on the item in the render window and selecting the "Is full LOD" box. That is a hotfix for said bug.