Ships don't have a mathematical requirement that their internal structure be one homogenous material, thus it's a trivial matter to put a weight at the lowest point of the ship so that it acts like a weeble: http://en.wikipedia.org/wiki/Weeble
Why? So they'll right themselves if they're capsized? If a ship (not a boat) capsizes you've got pretty serious problems already.
Besides, self-righting is a very different sort of problem when you're floating.
It is fairly standard for lifeboats to be self-righting. Google "self-righting boat" for examples. The typical shape is not a gömböc, though. A gömböc would self-right, even when completely under water.
The self righting designs I'm familiar with for (large) dinghies have a lot of lead in the bottom of the boat combined with a lot of built in buoyancy - they'd probably self right deep underwater.
I'm sure a gomboc would self-right when completely underwater, but what about a floating gomboc half-submerged? Different problem.
Also, ships are not solid (as in 'filled'), let alone uniform in density. On top of that, hydrodynamics imposes more important constraints on shape. You can make a ship pretty stable by loading its keel heavily.