Serpents should move deeper if the seabed allow this ( Disallow hovers to hover over them and see them ).
Your anti-sub hover could be a slow low-fire-rate unit with a low-range launcher or could fire targetable deepcharges.
Targetable deepcharges means, that you need more of them to effectively damage snakes - they can have low DPS because of a low fire rate too.
Because Snakes and Serpents move at a deeper altitude, they have time to fire the slow moving mines ( compare it with a bandit which is running away from a glaive )
because hovers aren't targetable for subs, we can also add a water-mine sub, which spams mines like volverine, but on the surface.
-> Sure they can also have a really low dps and can be used to counter penetrators or other low-HP targets, but should be very very inefficient.
At least they have to come close to your anti sub hovers and run into torp launcher things, but they can be used against all things on water.
Another option would be to make cloakable sub-pupies, which cost 200 metal each, and can't 'goo'.
It would also be nice to have dropable buildings - see the teleporter thread.
You have one sender and one receiver -> get the cheaper receiver to the target and let it "build/receive" the unit while the other part is "reclaiming/sending" this unit.
( to avoid abuse, it has to be fast, destroy both parts if unfinished, finish the building and the reclaiming at some percent before it would be finished anyway without need of the other part and block the teleported things for normal constructor interaction - damage while transport can be lethal )