[dnanian]

It's basically a very unusual situation. Because they were already "bad" - that is, what they were pointing to was different then their original target (by name/path, or even deleted), and they were using the "file number" to do a secondary reference (which may have been missing/empty). This can be made worse by a different volume name, since the alias includes the volume (so if your restored drive is called "Magic SSD" rather than "Macintosh HD", the situation often triggered).

When the alias finds itself on a different volume with the same conditions, the file number (which can't be recreated with a file-by-file copy) may be reused by some other file, and thus the alias can resolve itself to "something from nothing" or to something different on rare occasion.

Hard links to both files and folders are recreated as expected by SuperDuper, even if the inodes change (as they will). But aliases, being actual files themselves, are copied as-is. Why aliases don't use hard links on OS X is a mystery to me.