I'm not sure what happens when your sea terraforms lower terrain for tiles next to coastal bases. If you get a bunch, you might be able to sink a base in one turn. You might want an AA vessel or two to protect your stack, though there are planet busters and swarms.
One reason to get submersible terraformers, the weather paradigm, and the maritime project (+2 sea moves). Can send a probe sub destroyer (ignores ZOC; max range) or maybe needlejet radar units if they detect subs, to find a clear path for your terraformers before committing any actions.
I don't think planetbusters which leave sea tiles at epicenters count as drownings, but the after effects look the same.
I noticed there are missiles that cause earthquakes, raising terrain elevations, and also fungal payload missiles. Would it be a good SMAC addition to have EMP bombs? Could stimulate mindworm uprisings; disable tachyon fields or other base facilities (hologram theater) unless bases have some defensive facility (that has deep pressure dome as prerequisites. rational: need to upgrade a pressure dome vs EMP (and then you might require some advance warning system to raise the shields unless you're the hive)) for a turn; eliminate armor for photon armored units; maybe add a % chance to modify aircraft moves randomly per move (some chance planes lose moves that might normally allow them to safely return before crashing); eliminate energy production for a turn except from solar collectors /mirrors which get energy multiples; disrupt mag-tubes; reveal cloaked units in blast radius; nerf energy weapons (maybe a reason to keep producing +6 attack missiles from 200 years ago when others are using +24 super event horizon anti-nucleii dispersal conduits of telesubstantiation dialanctics). Also works well with would be 'secrets' (like drop a bunch of EMPs on fungal towers and they producing new mindworm strains or what). Could operate like based interceptors for planet busters (chance to intercept at the cost of that unit. chance to intercept increases with facilities, optionally surveillance (though surveillance is a bit much by game paradigm maybe). Maybe if you don't like the outcome of a planetary election there can be a button "EMP this ", giving you an extra turn or so to make bribes or implement other remediations (maybe if councils are EMPd enough times Santiago gets a power base no matter what and is planetary governor no matter what (there could be strategies for doing this: some percent of all bases get santiago control; all factions have permanent serve pacts with santiago. survivalists begin attacking (to conquer) all allied AIs that don't counterattack or what (conquest pattern like undead conquer the earth; or set that always at minimum santiago gets x% of bases/production, though there is no ceiling, if you want to keep civil war)))).
similar abstraction level to existing game elements a bit, and also EMPs are cannon for fighting video games.
edit:
I'd be intrigued by reports of fight simulations, starting with unarmored mildy armed infantry against max armored handweapons armed whatevers.
The idea, as is, for a smac emp bomb clashes with the combat mechanics facet of only considering armor of defenders. As conjectured, there would be no difference in combat outcomes between 6-1 vs 12-6 and 6-1 vs 1-6. The only immediate way would be to reduce armor value in relation to the attack value.
Another version would be to reduce attack values for the opponents turn, so if they want to counter attack with their 12-1-16 needlejets they find perhaps 1-1-16* (maybe reduce one move, and add 12% chance to veer off course in a random direction).
edit: re Frank Herbert inspiration:
In dune though everyone has high tech they use basic ballistics and hand weapons. The issued explanation discusses a convention to reduce arms technology because otherwise battle is reducible to total obliteration of any combat theater for both sides and anything formal in between (probably in general to be understood, though specifically there's some mention of how contact with some lazer guns with the Dune version of smac tachyon shields gets "atomics" with nuclear explosion reactions (is that a kind of cheeky joke? ...))
But a picture is while there are means of production for more sophisticated weaponry, more primitive weaponry is opted for, in relation to some discussion of 'practicality'.
A similar breakdown would be prominent in smac games with this kind of weapon. How's that? Lower tech 'ballistics' like synthetic fossil fuel lvl 6 rockets would be cheaper to produce than higher tech weapons, meaning you could make in the same amount of time with the same resources more missile units. One incentive not to do that in normal smac games is that the missile units fail against high armor, and then the opposition uses max weapons, which has an edge over your best armor, so the attack fails and armies get eaten in counter-attacks about.
With EMPs working my suggested way, advantage could be temporarily conferrable to the cheaper ballistics weapons in EMP blasted regions.
Implications are noticeable in emergent advantages for defense: at sight of an invading army, production can on the spot switch to the cheaper missile units, which are stronger per encounter with EMP support.
So if an intent is to conquer territory for someone else's home advantage, it's challenged by enabling of cheaper sufficient defense than offense, which favors skirmishes to conquest.
To defeat cheaper missile defense spam, an attacker could decide to make the cheaper ones also, which complements the existing psy combat strain. Optionally, stick with the more expensive units hoping that tactical/positional exploitation/initiative will thwart emp/ballistics, or maybe interceptor strategies hoping to embarass these armies by robbing them their EMP support and leaving them stranded vs otherwise superiorly armed enemies.