Two issues here.
The first is one of overcoming a ship's tendency to float. Since MGT doesn't address the mass of ships or the differing density of water at increasing depths or in different gravities, this has to be handled with some amount of handwaving. Possibly informed handwaving, if you know older editions, but handwaving none the less.
The mathematically exuberant TNE ship building rules of 20 years ago worked out to the point where minimally space-capable hulls (ie. "no armor") would float regardless of what machinery you put in them, while any level of armor considered worthy of military service was enough to take a hull past neutral buoyancy into "sinks like a rock" densities.
Acting counter to buoyancy if you are too heavy is easy: if you have working reactionless drives, any depth is attainable, including not under water at all. A ship that uses reaction drives needs to be adapted to under water operations, possibly with a whole new drive suite. Not a terribly big deal to a ship that routinely generates MW of power, but something to keep in mind.
Getting a floaty ship to sink also requires working drives, controlled inundation of the cargo deck (to hit neutral buoyancy), or both. If you need to sink but wouldn't normally, and can't use the cargo deck as a big dive tank, I would rule that 10 meters depth per G of maneuver drive is probably acceptable, with the understanding that loss of drives means you take a quick ride to the surface...
As for the other issue, crush depth of the hull, I would point at modern submarines. Properly constructed, any starship hull can perform the needed tasks of a pressure vessel. Traveller's history suggests strongly that any ship that flies will have no trouble with surface water, and that armored hulls can hide deep.
Most civilian hulls will, per two paragraphs above, never reach crush depth without taking water on board. It is safe to assume that a streamlined ship with "no armor" can probably drop to 30 meters, while unstreamlined hulls, not built to handle gas giant dives or even normal landings, are probably going to have issues by 10 meters. Treat each level of armor as a doubling of that number. Armor-1 gets you to 60m or 20m, while Armor-2 gets you to 120m or 40m. Not much armor is needed to let an SDB set on the bottom, sensor buoys/drones on the surface, waiting for law breakers...