I've been working on a deepwater survey shuttle. It needed some stuff that wasn't in the book, so here's what I came up with:
Specialized Hull: SUBMERSIBLE CAPABILITY
SU Cost: 1 x size
Power Cost: None
Most starships cannot submerge in liquids or extreme pressure gases; they're not built for it, so the pressure of diving into an ocean or lower levels of a gas giant crushes them (or at least causes substantial damage, though shield modifications can affect this). However, it is possible to build a ship with a specially designed and reinforced hull which allows for underwater movement. The necessary modifications occupy SUs equal to the ship's size, but cost no Power. Ships with submersible capability take no damage when entering or flying in deep water. A ship must have Outer Hull Resistance 6 or higher to be submersible-capable.
To make only the detachable part of a ship (like a separable saucer) submersible-capable costs only .25 x size (minimum of 1 SU).
To determine a ship's speed underwater, take its sublight speed rating, multiply by 100, and that is its speed in knots. IE, a ship capable of .5c in space can go 50 knots underwater. If a ship that is not submersible-capable is improvising with structural integrity fields and deflector shields to survive underwater, that speed should be halved. IE, .5c is good for 25 knots. Narrators may modify this number according to the sleekness of the design.