I think Taming Windows Defender will help with the crashing issues during import. There may have been rules in place for MC21 on the old Windows PC, but MC26 on the new PC is a different installation, and wouldn't have the rules. It is also a different executable, so Defender needs to be told how to properly handle it. If you installed MC26 on the older Windows PC you may see similar issues.
With Defender running it will analyse every file that MC touches during the import, which means a lot more work for the processor, which means more wait time for MC, and CPU load, and I think MC can trip up. Particularly if MC is doing other tasks during the import, such an Audio Analysis.
Yes, Synology runs on Linux.
The Hdden Files will just give MC more files to import, increasing load, making the situation worse. If MC tried to write tags to them that may also cause issues. I don't know. Hiding them could therefore indirectly help stop the crashing, but Defender needs to be tamed.
Also note that the ./ files might be (probably are) marked as System Files, and so may be harder to delete, requiring Administrator rights.