Those appear to be correct as far as the Game is concerned.
Even if in a Mission or a scripted Campaign file as a negative height?
They should not play the sinking effect.
For the most part,
A Ship scripted at a negative value will ignore the value and just run surfaced as normal.
This is easy to test in a single Mission.
Pick a Ship. Any Ship.
NO! NOT THAT ONE!
Script it at -15 for height at a speed of say 10 knots.
Then look at it in Game.