but in warfare, with all the hydra flak batteries around, unsupported air forays into enemy airspace is akin to suicide.
How is that different from naval actions? Ships are even more vulnerable since they are slow moving compared to planes and can thus be targeted by more conventional weapons. And who said they were going to be unsupported?
In many ways aircraft are more vulnerable than surface targets (in this case ships). As they have more elevation they can be shot from ground based weapons systems from further away, and indeed from above by orbital weapons. Sea based military, even in more technological advanced times still represent a highly efficient and safe way to move men and materials around a planet. While a thunderhawk gunship is a massive model in terms of 40k it's smaller, and carries less than a Galaxy-class transport plane we use today.
To fight a full ground war would require thousands of vulnerable fights and a huge outlay of fuel and resources. A safe landing zone would also be required along with depots, staging areas, barracks, ammo dumps etc. Most landing/beach assault ships have this capacity built in. And while resupplying and bolstering a front could be done by air the initial assault would be easier by sea. once a port is secured it can act as a landing zone of both ships and space based resources. Most modern navys merely act as a floating staging area now (although they hate to admit it).
Looking back at modern conflicts, armies today just can't move enough stuff by air to be effective.
Operation Market Garden air borne assault into France - Fail
Ohama beach - sea based assault into Normandy - Win
Desert storm - Initial artillery and missile strikes all sea based with almost all material being shipped by sea - Win
Indeed, look at the effort the Imperium goes to to mount titan-class weapons on well... titans. Huge slow moving behemoths that are now impossible for them to produce. The same power generation and weapon capacity would be far more easily mounted on a floating hull producing a truly terrifying battleship. To the same extent, apart from the railway guns of the great wars, the largest ordinance has always been ship mounted.
Anyway, the point being ships are vital to any military invasion. the moving of that much material forces commanders to use the sea. And as this supply line becomes the vulnerable point of a campaign, it would become one of the focus of any action. Unless the conflict involved races with significant anti-grav or teleportation/warp gate technology such as the Eldar or Necrons, the chances are it will have a seaborne aspect.
All this also precludes that the conflict is going to be fought on an yet another earth-type world where maritime assets consist of fishing and oil/gas production - assets of far less importance, and things hardly worth fighting over in the 40K universe. Some planets in the galaxy may have far greater water to land ratios with floating or undersea hive cities and production platforms. One of the reasons space marines fought with bolters in sealed power armour suits was their ability to function in all atmospheres including underwater.
So, now we come to the problems of a sea based game. The first is that the action is based in a far more three dimensional setting than a standard 40K game. Not only is the sea/board surface important, but so too are submersible units be they submarines, troops, or vehicles travelling on the sea bed. A diver with a chianfist is probably just as much a threat to a ship as a surface based ranged attack. So too are ariel units. skimmers and aircraft are deadly threats to sea based units. How this could be represented would pose quite a problem to any game designer.
How each of the races would approach their naval forces would also be interesting. As already mentioned, the Imperail Guard/PDF would mostly likely command such forces with space marines co-opting such units. Chaos would probably have corrupted ships crews many renegade ships along with ships summoned by dark sorceries such as the Floating Towers of Tzeeentch.
Presumably, there'd be Ork clans that based themselves at sea, with a mix of battleships and submersibles along with Cult of Speed crewed torpedo boats, zodiacs etc. On top of that a grechin manned giant-robot-shark is too good an idea to waste.
Tyranids would naturally have a whole host of bio-organisms. Indeed, the prospect of converting the majority of a planets bio-mass out of sight in the water would make a marine based attack on a world a primary facet of their invasions. Being able to drop gene-seed pods into the ocean where they'd quicky gestate and hatch into huge leviathans able to support enormas psychic brains that would broadcast the hive mind across the planet. Along with the kraken-like 'Nids would be schools of lesser hunters and predators ready for the command to metamorphose and become amphibious an attack the land. This could give the tyranids a very "Lovecraft-ian" feel with great Cthuliod monsters calling from the deep.
The Eldar and the Dark Eldar might have the technology to circumvent sea travel but not maritime assault. you could assume they would have aspect warriors dedicated to sea shrines or skimmers capable of landing on water.
The Necrons definitely possess the technology not to need waterborne craft, but who said that all their tombs were buried and not sunken? The Monoliths and destroyers would be unaffected by going over water and the warriors have no need to breathe so can travel beneath the waves.
I'm sorry if this is a bit of a rambling post, but i think like XCrusaderguy01 that a sea based game would be really cool, and would fit into the 40k universe.