[Duncan Idaho]

Ships I've sunk never vanish, unless they've blown up so bad that there's nothing left of them.

My 'killing fields' when I hunt are full of noisy corpses of ships, going underwater in free view you are treated to the sounds of many wrecks rumbling under the waves.

So I think that's just how it is. In fact, ship carcasses even return if you load a save game, so I don't think wrecks go away until the end of the patrol.