Sounds like there's a point to be made for referential integrity too. That is, if a struct contains string A twice, when you read it back in you'd want both those pointers to be identical. You'd get this for free with Cap'n Proto, but it would require extra care with "one-copy" or looser definitions of "zero-copy."
Heh, well, you could get it for free in Cap'n Proto if Cap'n Proto allowed pointer aliasing. It doesn't, though, because if it did, then messages would not be trees, they'd be graphs, which ruins a lot of stuff. For example, a very common thing to do with a message is copy one branch of the tree into a different message. Deep-copying a branch of a tree is easy. Deep-copying a branch of a graph, though -- what does that even mean?
For a DAG, maybe, but it requires a lot more bookkeeping. Now you have to remember all the pointers you've seen before in order to detect dupes. To do that you probably need a hash map and some dynamic memory allocation, ugh.
And what happens if you copy two different branches of one message into another, and they happen to share some children? Do you have to keep your seen-pointer map around across multiple copies?
For a cyclic graph, things get more confusing. Copying one branch of a fully-connected cyclic graph always means copying the entire graph. Apps can easily get into trouble here. Imagine an app that implements its own tree structure where nodes have "parent" pointers. If they try to copy one branch into another message, they accidentally copy the entire tree (via the parent pointers) and might not even realize it.
The one way that I think pointer aliasing could be made to work is if pointers that are allowed to alias are specially-marked, and are non-owning. So each object still has exactly one parent object, but might have some other pointers pointing to it from elsewhere. A copy would not recurse into these pointers; it would only update them if the target object happened to be part of the copy, otherwise they would have to become null.
But I haven't yet had any reason to try implementing this approach. And apps can get by reasonably well without it, by using integer indexes into a table.
This isn't a question of finding a magical solution, it's a question of trade-offs in performance, complexity, and usability that any solution necessarily imposes, and whether those trade-offs are worth it to support a feature that 99% of use cases don't need.
"Skyscrapers have been solved since the 20's" doesn't answer whether I should use steel beams when building a house.