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There is no water nor any space below the watersurface. Oceans are at height "0" and there is no negative height in the game. Because of that a sub can not submerge in that reality.

But a possibility may be to change a ship and make it look like a submerged sub (There is allready something like that in the game). A hitbox could be created by taking a bigger ship and making the overhangig parts transparent.

What about setting oceans at height +50 (say), with land masses above that? That might give a playable depth for subs (cloned AI aircraft with adjusted 3D models and suitable FMs). Just a thought...