I write 3D software including stuff for CNC machines and have done some stuff with terrain DEM files. I don't use STL myself for this purpose but I was wondering could you make the XYZ files using some scripts. For example, lets say your bathymetry data was of 2000x1000 grid for the sake of example. Could you create an XYZ file of a fixed small height of 2000x1000 for the base. Then create the layers from the data so as to make the walls. You have the side heights from row 0, row 999, col 0 and col 1999. Then use the same software to create a base STL object and 4 wall STL objects. Then you just need to merge all of them together. I know MeshLab could do that but I am not so familiar with the other apps.

Also, as a bit of an aside, do you have any of your data as a small swatch or sample of something not particularly relevant for this object but would show the kind of data you have on hand. Maybe a greyscale PNG depthmap file you might upload ? I used to work in sonar as well and have a little knowledge in that area too which may or may not be useful in your case but it depends on the kind of data you have to print.