I've written enough Clojure over the years to think that this is probably not the case. The reason this problem doesn't happen as much with Clojure is that the Clojure data structure is closer to JSON (and when using EDN instead of JSON, is identical.) If your serialization object model is close to your in-code object model, translating between the two is easy. If your serialization object model is distant from your in-code object model, then translation becomes difficult.

You can directly serialize and deserialize plain old Java objects to and from a native format and it's trivial to do so, but serializing to and from JSON is trickier because JSON is meant to represent dynamically typed data stored in maps and lists, but Java doesn't naturally store data in that manner. Java's manner is more obtuse, but if you could be certain that both the producer and the consumer of an object was going to be Java, creating a serialization format that could be transparently used would be a straightforward task. That is, so long as both the source and target of your serialization are in the same language, the problem is a lot simpler, and if your language happens to be closer Javascript (the source of JSON) it's also relatively simpler to write a JSON parser for it.