Tonnage and displacement tons for nautical ships has absolutely no direct relationship with Traveller tons.
Repeat - Tonnage and displacement tons for nautical ships has absolutely no direct relationship with Traveller tons.
They are in fact completely different measures - and displacement tons for nautical ships refers to displacement of water - which is dependent on mass and shape! It describes the volume of water displaced - and its definition varies widely, though 2.83 cubic meters might be the closest conservative equivalence (though, because of shape and water density, it can take higher values).
Further, there are loaded and unloaded displacement tonnages for nautical ships (because of mass and varying shape as waterline changes).
MGT tons is a lot simpler - its just volume of space (related to hydrogen volume of a given mass).
To calculate the MGT tons equivalent for the Yamoto would require actual dimensions of the ship - and cannot be derived or even well estimated from traditional nautical displacement tonnage.
Note also, that most dimensions only provide the height in terms of the water line - not to the deckline. And, other than barges and some freighters, the shape is so far removed from a 'box' that calculus would need to be used to come close to the actual volume.
All-in-all, it is rather useless to compare MGT spaceships, in almost any way, to nautical ships!
Submarines - given their typical shapes can be easily estimated (and submerged displacement tons could be used if one knows what type of tons and assumed water density were used).
A better comparison would be to skyscrapers! (And, for most, it would be a better visual comparison to size and far easier to calculate).