There is a lot more to booting an operating system than simply having a bunch of files on the disk. There's a reserved bunch of blocks at the start of the disk that contain some special boot instructions which tell the computer how to boot.

If your old hard drive isn't dead yet... I would highly recommend you look at a tool like clonezilla or Symantec Ghost to clone your hard drive. It will correctly copy the special bits of the drive that are needed to boot, as well as resizing the volume to fill the entire disk.

Calculating the size of hard links in Windows

It's difficult to calculate the size of hard-linked files in Windows. One tool that allows you to do this is TreeSize Professional (not free, analysis of hard links is switched off by default). I used this tool and it correctly estimated the size of the hard-linked files.

For a more thorough discussion, see How can I check the actual size used in an NTFS directory with many hardlinks?

Are the files actually working?

As for the other part of the question, is it risky to backup files using Linux tools under Windows on WSL? I decided to test this simply by copying one of the snapshot directories to a separate external hard drive. There were no problems copying the files, or reading them from the external drive. In other words, the hard links are behaving exactly as expected, and the files are working.

Long-term data stability

So down to the final point, could using Linux tools under WSL as part of my regular backups break something, such as corrupting the file system? Do I trust WSL not to break things majorly? Anything can break at any time, so I will make sure these snapshot directories get copied periodically to a separate drive.