There are two different tier one navy fabricators. Fabrication ships and fabrication subs, as far as i can tell they do exactly the same things and work the same way. I just build the subs because I like them I never see people build the combat submarine units, either they are not working correctly or they are severely underpowered. How do submarines react to things like air and land? Will air and land shoot submarines and will they shoot air and land? Is submarine path finding going to stay the way it is or will they gain the ability to "dive" under things like naval factories and units
certainly more units are to come i think deep sea units and structures is at hand for water planets. ony the sub fabber could construct those.
I don't think they are working correctly at the moment, but one would imagine the majority of units cannot shoot or even see subs.
Currently there is no underwater per say, but when there is surface units won't be able to attack deep sea units and buildings, making water control and subs valuable for attacking and defending players on water maps. Sub-fabbers are required to build those and subs to attack them.
In the future, subs won't be detectable without sonar. But right now they aren't working properly and aren't submersed, so they function like boats with less health. So - pointless and broken. But such is Alpha.