"Sea graves" are often protected sites for sunken military vessels, but there are relatively few passenger deaths at sea so there isn't a real urgency for lawmakers to defend places like the Titanic. Otherwise, wrecks that aren't protected become the 'property' of their discoverers and may be looted to a degree.
In the case of mummies, most every tomb had been robbed completely by the time Europeans arrived. That's why Tutankhamen is somewhat famous - his tomb was buried underground and undiscovered by grave robbers until its rediscovery. It is disrespectful to remove dead people, but it can be justified by arguing that if archaeologists don't remove the mummies, vandals or grave robbers will move in and disrespect the mummies even more -- you can't defend thousands of graves throughout Egypt 24/7 forever.
edit: There are indeed grave sites in the ocean, at least according to the United Kingdom:
http://en.wikipedia.org/wiki/Protection_…