So one approach to fix that would be to ask Windows to expand the path at import time. This way if you imported from S:\, it would just get automatically expanded to \\Linux\pc. This would totally solve the duplicate problem.
I would prefer my files to be imported on the same path I told MC to look for them, and not to do anything weird to them. IMHO software should behave on the principle of "least surprise", and it changing the path under me would be rather surprising.
A drive may not be the same everywhere - for example, in my setup: My "S:\" drive (really Z:\ for me) is a locally mapped drive on the server (using the handy "subst" command), while on the clients its a mapped network drive - that way the server can avoid to go through the network stack to read files, and only the clients will do that.
Another thing, at one point in time, I rebuild my server that MC was running on, so for migration purposes both old and new were running at the same time - I could just change the mapped drive to point to the new server, and everything worked out of the box. With this, I would have to fix every single library entry.