It's been many years since I last used sh404SEF, but I can think of a few things:
1. Have you manually excluded any tables from your site? If you did, you may want to remove the exclusion from sh404SEF's tables.
2. Did you have to purge SEF URLs after restoration to get your site working? I assume that when you purge the URLs, all the meta information per page get purged.
3. It is possible that sh4040SEF stores the meta information per URL and if the URL changes (e.g. moving to a different domain, subdomain or subdirectory) that would mean that this meta info is lost.
Since this seems to be an issue with the way sh404SEF works and not something with Akeeba Backup (Akeeba Backup will either back up a table or skip it, depending on what you tell it to do) I would suggest contacting the helpful guys at Anything Digital with this question. They will be able to tell you what you need to do to keep the meta information when you backup and restore your site