Some people dislike the idea of spaceships submerging in general, citing Professor Farnsworth from Futurama saying that they're only built to handle atmospheric pressures between 0 and 1. I think some planets have thicker atmospheres, and don't necessarily subscribe to this thinking
I think its important to understand why the pressure is a problem for starships that can otherwise survive anti-tank weapons.
Starships are built to have more pressure on the inside than on the outside.
This is part of the reason why aluminum cans are so strong before they've been opened. All that pressure pushing on the thin outer skin reinforces the whole thing.
Another thing to keep in mind is that because the pressure is greater on the inside, generally you're going to build all your external doors to open inward. This means all the pressure from the ship is forcing those external doors closed. Your doors are also probably a bit bigger than the hole they are covering, so all that pressure helps force that overlap closed so nothing leaks out.
If you flip this around, and all the pressure is on the outside of the ship, you now have to design everything to account for that. Your poor engineers have to massively over engineer all the coverings, doors, inlets, and sensitive outer parts to withstand being pushed together by outside pressure and pushed apart by interior pressure. Just like any door, it is a lot easier to push open than to pull open.
You also have other problems when moving at speed under water like cavitation eating away at anything exposed to fluid moving across it. This will damage your stealth coatings, your radiators, your sensors, and even your armor.
It is also very likely that your areodynamic shapes don't work so well when submerged, again due to pressure.
Of course you could turn on your shields and negate this whole problem by just not actually being in the water, and holding a bubble of air around the craft at the right pressure... but still.
Unshielded is probably a very slow top speed: maybe 200kmph
Shielded: Probably a mach 1 or 2?
And any ship designed to supercavitate would likely just use their atmospheric top speed.