Gravity isn't going to do much for an aquatic species anyway; they'd be accustomed to the buoyancy effect offered by oceanic environments. The entirety of the ship doesn't need to be flooded either, only sections that the crew (if the ship even has one) will be occupying. Electrical systems can be easily water-proofed if needed, which is an obstacle I'd expect a water-bound species to have defeated long before they even made it into space. Ship size doesn't exactly have to be massive, though duel-purposing a spacecraft for deep sea activity may be problematic if only because of how submarines works (if a critical hull breach occurs, the submarine is more or less destined for destruction).

Sufficient amounts of handwavium would be acceptable; warfare for the space merfolk wouldn't be especially difficult, mostly because there's no real reason why it should be.