But I don't think you'd have this problem. Just like we have an inode telling every block of a file, a filesystem like that would need a similar structure telling every hash of the file. When you delete a block, you look at this structure, the same way you look at an inode.
The only thing missing is that you'll need a counter at the blocks. And this counter will create some synchronization problems that may turn out more important than saving disk space.
But I don't think you'd have this problem. Just like we have an inode telling every block of a file, a filesystem like that would need a similar structure telling every hash of the file. When you delete a block, you look at this structure, the same way you look at an inode.
The only thing missing is that you'll need a counter at the blocks. And this counter will create some synchronization problems that may turn out more important than saving disk space.