If I understand magnet protocol correctly, it doesn't matter. If two files are the same, they have the same hash, so the system (DHT) cannot tell them apart.
If the files are different (e.g. 256 and 320 bitrate mp3 files), then that is a completely different problem.
I should have been precise: how does one determine the number of seeds for a given piece of data e.g. when the same movie at different resolutions is available, that is, different hashes?
I think that when you use a magnet link it either includes the tracker (which is the part of BitTorrent that tracks the seeds) in the text of the link or uses a more sophisticated technology called a Distributed Hash Table.
If the files are different (e.g. 256 and 320 bitrate mp3 files), then that is a completely different problem.