I think this is certainly an appropriate use of building=ship, but the wiki entry doesn't seem to address whether the ship should be an inner relation of the water or not.  Examples seem to be split both ways.

Absent a consistent standard, I think your logic that the ship sits on top of the water is a good one and would concur with removing it from the relation.

Museum ships that are an inner relation of the surrounding water:
USS New Jersey
https://www.openstreetmap.org/way/29667862
USS Olympia
https://www.openstreetmap.org/way/170349584
USS North Carolina
https://www.openstreetmap.org/way/45666397

Museum ships that are not a inner relation member of water
USS Chesapeake
https://www.openstreetmap.org/way/127075950
USS Torsk
https://www.openstreetmap.org/way/109484023
USS Yorktown, Laffey, & Clamagore
https://www.openstreetmap.org/way/39010151
HMS Queen Mary
https://www.openstreetmap.org/way/438331516