This has long been a complaint that has been brought up on occasion. In RA_HostileWaters, Raap addressed this in the Advanced Sub Pen by placing grated walking platforms over the water where the sub spawned. Because you have to actually jump on top of the sub to get inside (don't know if the entry point can be easily changed because of water logic in W3D, I feel like there might be some funky reason why not), he decided to make the opening in the grate small enough that you could safely stand on the sub without falling in the water. I have yet to see someone lag into the water while trying to enter a sub in that particular building. Maybe its possible that the standard Sub Pen could undergo a slight overhaul in which some similar grates could be added to prevent this in a similar fashion? Shouldn't be too difficult. As far as the ladders underwater, that might also depend on how well the logic for those components play together. I don't have any knowledge of how these things work, I just remember past instances in testing where water totally screwed up something that otherwise worked absolutely fine, ie gap clouds.
I'll let pushwall or someone else more knowledgeable than myself speak on this though