In the rules for Thunder bombs, it says that land-based mines dropped in a water hex sink to the bottom and operate normally there. It's not listed elsewhere, but it seems logical to me that LRM or artillery-delivered Thunders would work the same way.
The rules for conventional sea mines say they only struck units at their depth. You might want to ask in the rules forum, but my reading would be that land mines on the sea floor would only struck units moving along the bottom, such as mechs or sealed tanks. You want to hit a boat or sub, you have to put mines on the surface, or an expected depth.
