Hi @Robertoal and welcome to the community!
Wow, this sounds like an exciting and challenging project! From the 2D cuts, I would expect that something like the average angle of the shore is already a good predictor whether a shore is NFS or not. I’d expect ML would probably only be interesting to classify the cuts into more types of shore. But as you said, the challenge for now is to automatically preprocess your data to get out a the shorelines for each position. Your general plan of attack looks quite sound to me; regarding the tools to use let me give my 5 cents to it:
Honestly, I’m not quite sure whether I would recommend to use (only) KNIME for that: Determining the river trajectory (I understand you have these already?), calculating the normal vectors (with splines?) and creating the section cuts from the 3D map sound more like tasks for python to me. I personally would use the jupyter notebooks to do the python development part, as they allow for easy visualization in between steps.
Once you have a (training)-table with the cross sections, label with the shore type, shore side (L/R), shore identifier (long&lat),… , you’d need to decide which model to use for classification (as mentioned, if the average shore angle is not already a well enough predictor): this is where KNIME could be the right tool to use - especially the AutoML component could be interesting for you there. (Of course, you can always incorporate the python part with a python source/script node and go on in KNIME from there 
).
Regarding your two questions (since I think your plan of attack is excellent):
- As said, I’d create the cross sections with Python. The other part of the the question aims at how to map the river trajectory to the 3D river data, right? This depends on the data itself, but I would assume that the 3D data comes with some sort of location identifier? With that you should be able to map the xy(z)-3D-map vertices to the x-y-data of the trajectory.
- Performance-wise this shouldn’t really be an issue, neither in KNIME nor in Python.
Hope that helps!
Best, Lukas