Seagoing ships are good at being in salt water but don't deal as well with being engulfed in plasma. Starship is pretty good at being engulfed in plasma but doesn't handle being engulfed in salt water very well. Making a single ship that can handle both is a very tall order, even just doing one or the other is hard.
Seagoing ships are pretty good at floating on top of salt water for a while, but they're not very good at being "dunked" in it (i.e. sunken). It is possible to raise sunken ships and rehabilitate them to regular service, and this has been before, but it generally destroys everything inside, and requires a ton of work. Salt water is one of the most corrosive substances we know of.
Dunked in the ocean. There just isn't a ton of plasma and it's not very good at transferring heat to things it isn't being pressed up against. So heat shields and the like function very well. Seawater by contrast gets everywhere, and if it does even a little damage, keeps doing it for a long time.
A lot of the damage happens as soon as the spacecraft enters the water, because it's extremely hot, causing more chemical reactions than you might think. Even jet engines have trouble with corrosion from ingesting small amounts of aerosolized salt water.[1]
- time to transport, move back into initial position.