Carlo, your descriptions of your setup are excellent. Based on those, you shouldn't be having any trouble. You should probably run the JRiver Benchmark (Help > Benchmark) and report the result for your machine.
I am wondering if there is some corruption in your Library. Given that the single NAS libraries you created work fine and are quite large, corruption could be the case. Identifying that and fixing it could be difficult.
You could try;
1. Backing up the original 349,000 file Library.
2. Clearing that Library using the function under the Library Manager, which is under Playing Now, or on the menu under "File > Library > Clear Library".
3. Restoring the backup you just made, including settings.
The Restore process may fix any corruption by ignoring bad records, but that is a bit of a guess on my part.
The only other way I know to fix a broken Library would be to make sure all tags are written to media files and/or Sidecar files, export all views and Playlists, then clear the Library and re-import everything, including Playlists and Views. But that would be a long process, and if you have custom fields and Views it may not be particularly successful.
The other thing you could try to do is identify what process is causing MC to become non-responsive. You could use the Windows Task Manager and Resource Manager to see if anything is obvious, or get Microsoft's "
Process Explorer" and see if you can identify the problem. That is a complex path to take though, and time consuming, even just to learn how to use Process Explorer. I would be looking at network and CPU load when the problem happens, and maybe GPU load as well. You will need something like GPU-Z to view GPU load.
That is about all I can suggest at the moment. Maybe someone else has some other ideas.