The other reason I don't allow landfilling submerged ores is that the visual appearance of ore submersion is automatic because it uses a transparency effect, which would look very awkward against surface tiles; I could potentially solve this by "hiding" the ore inside a dummy object somehow and then returning it if tiles are removed, but that would require complex scripting for a very niche feature.
Allowing the mining of seafloor ores with standard drills also has the nice consequence that if you're mining a patch at the edge between land and sea, a drill that covers the general area will be able to extract both without having to patch in additional drills for areas that would otherwise be covered.