Unlinking logic from a weapon menu related computer (weapons, support tools, rail dockers, ...), either manually or by destroying the logic block, does not automatically restore this old shipcore-computer link.
It's more of an ease of access issue than a real bug.
If the computer auto links to the ship core, no one will realize that link exists. If no one realizes this, restoring the shipcore - computer link yourself after disconnecting logic from it, is not a logical conclusion as you expect the game to take care of that.