If not just used for decoration, it could hold salt or spices (the latter being very expensive in the Middle Ages), or cutlery, or even napkins.
The large nef depicted in the well-known calendar miniature for January from the Très Riches Heures du Duc de Berry is being used to hold, and perhaps wash, gilt dishes from the table service.
The so-called Mechanical Galleon in the British Museum is a late 16th-century German nef which was also a clock and automaton, with moving figures and music.
A nautilus shell often formed the hull of the ship, as in the Burghley Nef (illustrated).
The equivalent in religious plate is a navicula, Latin for small ship, and also a term in English for a boat-shaped incense-holder.