Hi Stefano,
My understanding is once NTFS has 1023 hard links to a file it creates a new copy of the file and starts creating hard links to that. If you have 4000 links to the file NTFS will create 4 copies of the file.
To answer your question the backup will be good.
The only issue is the backup will take more space.
Keep in mind that NTFS slows when the MFT gets big (lots of files on drive). You can format the drive to prevent multiple MFTs.