My guess is that resources that spawn under water are removed and respawn, but that this process have some delay, kinda like the mobs thats drowning...
The ability to place mining bombs underwater is removed as the number of deposits underwater is very scarce after the release. So this is a precaution to avoid excessive bombing in a low-yield area.
I found enogh deposits underwater (bombing on the beach), more than one time, even respawned in same place, to not believe their statement regarding "scarced deposits". Either they have no idea how the ore respawns, either they prepare some surprise.
I found lots of deposits in this VU underwater. I think MA just moved all the deposits closer to shore so there are none in deep water anymore. In past VUs I never found that much far out from shore. Maybe in the future MA will bring ocean mining back with some new water mobs and maybe a city or two.