Hi NH.
In the past, I have worked too with model data following the same structure you describe, that is:
-topology or coordinates (x,y,z) and
-(multiple) scalar field(s), such as temperature, pressure or velocity components.
What I did to visualize it was described in a few blog post in the forum (see links below), to recreate large scale scenarios for my atmospheric model (WRF). As an example, I have demonstrated how the same applies for ocean model (ROMS), where Z axis is pointing down (below water).
You can either work directly with netcdf (model output) or, if you need custom manipulation and reprocessing, you can generate your own vtk (I did that in python).
The blog posts have some code included. I hope you will find it interesting. The links are:
Also, there are some video on YouTube I created some 5 years ago showing just that. Just search for "swash wave model paraview). This is one example:
Hope this helps.